Structure of LP2179, the first representative of Pfam family PF08866, suggests a new fold with a role in amino-acid metabolism.
ABSTRACT The structure of LP2179, a member of the PF08866 (DUF1831) family, suggests a novel α+β fold comprising two β-sheets packed against a single helix. A remote structural similarity to two other uncharacterized protein families specific to the Bacillus genus (PF08868 and PF08968), as well as to prokaryotic S-adenosylmethionine decarboxylases, is consistent with a role in amino-acid metabolism. Genomic neighborhood analysis of LP2179 supports this functional assignment, which might also then be extended to PF08868 and PF08968.
- SourceAvailable from: Thomas Charles Terwilliger[show abstract] [hide abstract]
ABSTRACT: Obtaining an electron-density map from X-ray diffraction data can be difficult and time-consuming even after the data have been collected, largely because MIR and MAD structure determinations currently require many subjective evaluations of the qualities of trial heavy-atom partial structures before a correct heavy-atom solution is obtained. A set of criteria for evaluating the quality of heavy-atom partial solutions in macromolecular crystallography have been developed. These have allowed the conversion of the crystal structure-solution process into an optimization problem and have allowed its automation. The SOLVE software has been used to solve MAD data sets with as many as 52 selenium sites in the asymmetric unit. The automated structure-solution process developed is a major step towards the fully automated structure-determination, model-building and refinement procedure which is needed for genomic scale structure determinations.Acta Crystallographica Section D Biological Crystallography 05/1999; 55(Pt 4):849-61. · 14.10 Impact Factor
- [show abstract] [hide abstract]
ABSTRACT: The FFAS03 server provides a web interface to the third generation of the profile-profile alignment and fold-recognition algorithm of fold and function assignment system (FFAS) [L. Rychlewski, L. Jaroszewski, W. Li and A. Godzik (2000), Protein Sci., 9, 232-241]. Profile-profile algorithms use information present in sequences of homologous proteins to amplify the patterns defining the family. As a result, they enable detection of remote homologies beyond the reach of other methods. FFAS, initially developed in 2000, is consistently one of the best ranked fold prediction methods in the CAFASP and LiveBench competitions. It is also used by several fold-recognition consensus methods and meta-servers. The FFAS03 server accepts a user supplied protein sequence and automatically generates a profile, which is then compared with several sets of sequence profiles of proteins from PDB, COG, PFAM and SCOP. The profile databases used by the server are automatically updated with the latest structural and sequence information. The server provides access to the alignment analysis, multiple alignment, and comparative modeling tools. Access to the server is open for both academic and commercial researchers. The FFAS03 server is available at http://ffas.burnham.org.Nucleic Acids Research 08/2005; 33(Web Server issue):W284-8. · 8.28 Impact Factor
- [show abstract] [hide abstract]
ABSTRACT: Many bacteria can form aggregates on interfaces, called biofilms, where they are much more protected against toxic agents such as antibiotics or antibodies. Bacteria organized in biofilms are therefore very difficult to control and often even high dosages of antibiotics cannot clear infectious biofilms. To form biofilms bacteria have to start a complex genetic program to switch from planktonic to sessile lifestyle. This starts with the determination of their cell density, a process called quorum sensing, triggered by small, water soluble molecules, so called autoinducers. From Gram-positive bacteria several small peptides are known, many of them thiolactones. More recently another group of compounds was discovered probably formed from ribose-homocysteine and the first autoinducer-II identified is a furanosyl borate diester. While small peptides are found to trigger the intraspecies communication autoinducer-II is assumed to be used for communication at the interspecies level. Taking the lead structure from these peptides several derivatives have been developed which prevent biofilm formation in many Gram-positive bacteria, including Staphylococcus aureus. Some of these compounds are already in clinical studies. In this review the different approaches to control bacterial biofilms are discussed together with the difficulties arising from the species-specificity of the autoinducers.Current Medicinal Chemistry 02/2006; 13(13):1509-24. · 4.07 Impact Factor
Acta Cryst. (2010). F66, 1205–1210doi:10.1107/S1744309109023689
Acta Crystallographica Section F
Structure of LP2179, the first representative of Pfam
family PF08866, suggests a new fold with a role in
Mitchell D. Miller,a,cS. Sri Krishna,a,b,e
Herbert L. Axelrod,a,cHsiu-Ju Chiu,a,c
Thomas Clayton,a,dMarc C. Deller,a,d
Lian Duan,a,eMarc-Andre ´ Elsliger,a,d
Julie Feuerhelm,a,fSlawomir K.
Grzechnik,a,eJoanna C. Grant,a,f
Gye Won Han,a,dLukasz
Jaroszewski,a,b,eKevin K. Jin,a,c
Heath E. Klock,a,fMark W. Knuth,a,f
Piotr Kozbial,a,bDavid Marciano,a,d
Daniel McMullan,a,fAndrew T.
Linda Okach,a,fSilvya Oommachen,a,c
Jessica Paulsen,a,fRon Reyes,a,c
Christopher L. Rife,a,cHenry J. Tien,a,d
Christina V. Trout,a,dHenry van den
Xu,a,cKeith O. Hodgson,a,gJohn
Wooley,a,eAshley M. Deacon,a,cAdam
Godzik,a,b,eScott A. Lesleya,d,fand
Ian A. Wilsona,d*
aJoint Center for Structural Genomics,
http://www.jcsg.org, USA,bProgram on
Bioinformatics and Systems Biology, Burnham
Institute for Medical Research, La Jolla, CA,
USA,cStanford Synchrotron Radiation
Lightsource, SLAC National Accelerator
Laboratory, Menlo Park, CA, USA,dDepartment
of Molecular Biology, The Scripps Research
Institute, La Jolla, CA, USA,eCenter for Research
in Biological Systems, University of California,
San Diego, La Jolla, CA, USA,fProtein Sciences
Department, Genomics Institute of the Novartis
Research Foundation, San Diego, CA, USA, and
gPhoton Science, SLAC National Accelerator
Laboratory, Menlo Park, CA, USA
Correspondence e-mail: email@example.com
Received 15 May 2009
Accepted 19 June 2009
PDB Reference: LP2179 from L. plantarum,
The structure of LP2179, a member of the PF08866 (DUF1831) family, suggests
a novel ?+? fold comprising two ?-sheets packed against a single helix. A
remote structural similarity to two other uncharacterized protein families
specific to the Bacillus genus (PF08868 and PF08968), as well as to prokaryotic
S-adenosylmethionine decarboxylases, is consistent with a role in amino-acid
metabolism. Genomic neighborhood analysis of LP2179 supports this functional
assignment, which might also then be extended to PF08868 and PF08968.
The Pfam database (Finn et al., 2008) contains over 2000 domains of
unknown function (DUFs), which are protein families for which the
biological function is unknown and cannot be deduced by homology.
Currently, DUFs are the best source for the discovery of new folds
(Jaroszewski et al., submitted), followed by large families with no
structural representatives. DUF structures provide the first step
towards establishing functional hypotheses and extending our
understanding of the protein universe. In an effort to sample and
understand the diversity of protein-fold and structure space, targets
were selected from Pfam protein family PF08866 (DUF1831). Here,
we report the crystal structure of LP2179, the first structural repre-
sentative of this family, which was determined using the semiauto-
mated high-throughput pipeline of the Joint Center for Structural
Genomics (JCSG; Lesley et al., 2002) as part of the NIGMS Protein
Structure Initiative (PSI; http://www.nigms.nih.gov/Initiatives/PSI/).
The LP2179 gene of Lactobacillus plantarum, a lactic acid-producing
bacterium found in human saliva and intestinal flora, encodes a
protein with a molecular weight of 12.6 kDa (residues 1–113) and a
calculated isoelectric point of 8.9. LP2179 appears to adopt a novel
fold with remote similarities to proteins with a TBP-like fold (TATA-
binding protein), including S-adenosyl-l-methionine decarboxylase
(EC 188.8.131.52), an enzyme implicated in the urea cycle and the cata-
bolism of methionine and amino groups. Analysis of the genomic
neighborhood of DUF1831 homologs reveals the systematic presence
of other enzymes implicated in amino-acid and amino-group meta-
bolism, suggesting a similar role for other members of the DUF1831
family and for two other functionally uncharacterized families that
show partial structural similarity to LP2179.
2. Materials and methods
2.1. Protein production and crystallization
Clones were generated using the Polymerase Incomplete Primer
Extension (PIPE) cloning method (Klock et al., 2008). The gene
encoding LP2179 (GenBank NP_785678, gi:28378786, Swiss-Prot
Q88V95) was amplified by polymerase chain reaction (PCR) from
L. plantarum WCFS1 NCIMB8826 genomic DNA using PfuTurbo
DNA polymerase (Stratagene) and I-PIPE (Insert) primers (forward
30; reverse primer, 50-aattaagtcgcgttaGTCCGTCGTGAGGATATC-
CCGTTC-30; target sequence in upper case) that included sequences
for the predicted 50and 30ends. The expression vector pSpeedET,
which encodes an amino-terminal tobacco etch virus (TEV) protease-
cleavable expression and purification tag (MGSDKIHHHHHH-
ENLYFQ/G), was PCR-amplified with V-PIPE (Vector) primers
(forward primer, 50-taacgcgacttaattaactcgtttaaacggtctccagc-30; reverse
primer, 50-gccctggaagtacaggttttcgtgatgatgatgatgatg-30). V-PIPE and
I-PIPE PCR products were mixed to anneal the amplified DNA
fragments together. Escherichia coli GeneHogs (Invitrogen) com-
petent cells were transformed with the V-PIPE/I-PIPE mixture and
dispensed onto selective LB–agar plates. The cloning junctions were
confirmed by DNA sequencing. Expression was performed in a
selenomethionine-containing medium. At the end of fermentation,
lysozyme was added to the culture to a final concentration of
250 mg ml?1and the cells were harvested and frozen. After one
freeze–thaw cycle, the cells were sonicated in lysis buffer [50 mM
HEPES pH 8.0, 50 mM NaCl, 10 mM imidazole, 1 mM tris(2-car-
boxyethyl)phosphine–HCl (TCEP)] and the lysate was clarified by
centrifugation at 32 500g for 30 min. The soluble fraction was passed
over nickel-chelating resin (GE Healthcare) pre-equilibrated with
lysis buffer, the resin was washed with wash buffer [50 mM HEPES
pH 8.0, 300 mM NaCl, 40 mM imidazole, 10%(v/v) glycerol, 1 mM
TCEP] and the protein was eluted with elution buffer [20 mM
HEPES pH 8.0, 300 mM imidazole, 10%(v/v) glycerol, 1 mM TCEP].
The eluate was buffer-exchanged with TEV buffer (20 mM HEPES
pH 8.0, 200 mM NaCl, 40 mM imidazole, 1 mM TCEP) using a PD-10
column (GE Healthcare) and incubated with 1 mg of TEV protease
per 15 mg of eluted protein. The protease-treated eluate was run over
nickel-chelating resin (GE Healthcare) pre-equilibrated with HEPES
crystallization buffer (20 mM HEPES pH 8.0, 200 mM NaCl, 40 mM
imidazole, 1 mM TCEP) and the resin was washed with the same
buffer. The flowthrough and wash fractions were combined and
concentrated to 10 mg ml?1by centrifugal ultrafiltration (Millipore)
for crystallization trials. LP2179 was crystallized by mixing 200 nl
protein solution with 200 nl crystallization solution in a sitting-drop
format over a 50 ml reservoir volume using the nanodroplet vapor-
diffusion method (Santarsiero et al., 2002) with standard JCSG
crystallization protocols (Lesley et al., 2002). Crystals from two
different crystallization conditions were used for data collection and
structure determination. The crystallization reagent yielding a cube-
like crystal (0.1 ? 0.1 ? 0.1 mm) used for MAD phasing consisted of
20.0%(w/v) PEG 6000 and 0.1 M Bicine pH 9.0 as the precipitant. A
long rod-like crystal (0.3 ? 0.1 ? 0.1 mm) used for refinement was
obtained using 0.2 M NaCl, 20.0%(w/v) PEG 8000 and 0.1 M CAPS
pH 10.5. Crystallization was carried out at 277 K for both conditions.
Glycerol was added to both crystals as a cryoprotectant to a final
concentration of 15%(v/v). Initial screening for diffraction was
carried out using the Stanford Automated Mounting system (SAM;
Cohen et al., 2002) at the Stanford Synchrotron Radiation Light-
source (SSRL, Menlo Park, California, USA). Both sets of diffraction
data were indexed inthe orthorhombic spacegroup P212121(Table 1).
The oligomeric state of LP2179 was determined using a 0.8 ? 30 cm2
Shodex Protein KW-803 column (Thomson Instruments) pre-cali-
brated with gel-filtration standards (Bio-Rad).
2.2. Data collection, structure solution and refinement
Multiple-wavelength anomalous diffraction (MAD) data were
collected at the Advanced Photon Source (APS, Argonne, Illinois,
USA) on beamline 23-ID-D at wavelengths corresponding to the
high-energy remote (?2), inflection (?3) and peak (?4) of a selenium
MAD experiment. Higher resolution data from a different crystal
were collected at the Advanced Light Source (ALS, Berkeley, Cali-
fornia, USA) on beamline 8.2.2. The data sets were collected at 100 K
using a MAR Mosaic 300 detector (APS) and an ADSC Quantum-
315 CCD detector (ALS). The MAD data were integrated and
reduced using XDS and then scaled with the program XSCALE
(Kabsch, 1993). The higher resolution (?1) data were integrated and
reduced using MOSFLM (Leslie, 1992) and then scaled with the
program SCALA (Collaborative Computational Project, Number 4,
1994). Phasing of the MAD data was performed with SOLVE
(Terwilliger & Berendzen, 1999; four selenium sites per asymmetric
unit, mean FOM = 0.52) and automated model building was
performed with ARP/wARP (Cohen et al., 2004). The resulting model
was used for model completion and refinement against the higher
resolution (?1) data with Coot (Emsley & Cowtan, 2004) and
REFMAC 5.2 (Murshudov et al., 1999). Data reduction and refine-
ment statistics are summarized in Table 1.
2.3. Validation and deposition
Analysis of the stereochemical quality of the model was accom-
plished using AutoDepInputTool (Yang et al., 2004), MolProbity
(Davis et al., 2004), SFCHECK 4.0 (Collaborative Computational
Project, Number 4, 1994) and WHATIF 5.0 (Vriend, 1990). Protein
Bakolitsa et al.
Acta Cryst. (2010). F66, 1205–1210
Summary of crystal parameters, data-collection and refinement statistics for
LP2179 (PDB code 2iay).
Values in parentheses are for the highest resolution shell.
?2MADSe ?3MADSe ?4MADSe
Unit-cell parameters (A˚)
a = 36.29,
b = 47.90,
c = 58.01
a = 36.41, b = 47.99, c = 57.83
Resolution range (A˚)
No. of observations
No. of unique reflections
Rmergeon I† (%)
Rmeason I‡ (%)
Model and refinement statistics
Resolution range (A˚)
No. of reflections (total)
No. of reflections (test)
Data set used in refinement
Restraints (r.m.s.d. observed)
Bond angles (?)
Bond lengths (A˚)
Average isotropic B value (A˚2) 8.86
ESU†† based on Rfree(A˚)
Water molecules/other solvent
|F| > 0
number of unique reflections used in refinement was slightly less that the total number
that were integrated and scaled. Reflections were excluded owing to systematic absences,
negative intensities and rounding errors in the resolution limits and unit-cell
calculated and observed structure-factor amplitudes, respectively. Rfreeis the same as
Rcryst but for 5.1% of the total reflections chosen at random and omitted from
refinement†† Estimated overall coordinate error (Collaborative Computational
Project, Number 4, 1994; Tickle et al., 1998).
ijIiðhklÞ ? hIðhklÞij=P
hkl½N=ðN ? 1Þ?1=2
§ Typically, the
ijIiðhklÞ ? hIðhklÞij=P
iIiðhklÞ (Diederichs & Karplus, 1997).
??jFobsj ? jFcalcj??=P
hkljFobsj, where Fcalcand Fobsare the
quaternary-structure analysis used the PISA server (Krissinel &
Henrick, 2007). Fig. 1(c) was adapted from an analysis using PDBsum
(Laskowski et al., 2005) and all other figures were prepared with
PyMOL (DeLano Scientific). Atomic coordinates and experimental
structure factors for LP2179 at 1.20 A˚resolution have been deposited
in the PDB under accession code 2iay.
3. Results and discussion
3.1. Overall structure
The crystal structure of LP2179 (Fig. 1a) was initially determined
to 1.33 A˚resolution using the multiple-wavelength anomalous
dispersion (MAD) method and was further refined to 1.20 A˚reso-
lution using data collected from a different crystal. Data-collection,
model and refinement statistics are summarized in Table 1. The final
model includes 114 residues (i.e. the residual Gly0 from the expres-
sion tag followed by residues 1–113 of LP2179), one glycerol mole-
cule, one chloride ion and 195 water molecules in the asymmetric
unit. The side chains of Lys8, Lys59 and Lys86 were not modeled
owing to poor electron density. The Matthews coefficient (VM;
Matthews, 1968) is 2.0 A˚3Da?1and the estimated solvent content is
37.2%. The Ramachandran plot produced by MolProbity (Davis et
al., 2004) shows that 98.2% and 100% of the residues are in favored
and in favored and additionally allowed regions, respectively.
LP2179 forms a single domain composed of two antiparallel
?-sheets packed against a long C-terminal helix H3 (Fig. 1). A second
helix, H1, links strand ?2 from the first ?-sheet (order 127), which is
assembled from the two N-terminal and the C-terminal ?-strands,
to the second ?-sheet (order 3456) and packs parallel to H3.
Pre-SCOP classifies LP2179 as a novel fold termed LP2179-like
of the crystallographic packing of LP2179 using the PISA server
(Krissinel & Henrick, 2007) and analytical size-exclusion chromato-
graphy in combination with static light scattering indicate that a
monomer is the likely quaternary form.
3.2. Comparison with other structures
A search with FATCAT (Ye & Godzik, 2004) revealed a remote
structural similarity of LP2179 to members of the YugN-like family
(PF08868), which are characterized by a TBP-like fold (http://
www.mrc-lmb.cam.ac.uk/agm/pre-scop/55944. html). Superposition of
LP2179 onto ABC2387 (PDB code 2pww; U. A. Ramagopal, J.
Freeman, C. Lau, R. Toro, K. Bain, L. Rodgers, J. M. Sauder, S. K.
Burley & S. C. Almo, unpublished work), a YugN-like homolog from
Bacillus clausii, clearly reveals that both proteins share the same fold
and topology over all of the helices and strands ?3–?5 from the
second ?-sheet (strands ?3–?6; Fig. 2a). The structural similarity
involves a main-chain r.m.s.d. of 2.5 A˚over 81 residues, although the
Acta Cryst. (2010). F66, 1205–1210Bakolitsa et al.
Crystal structure of LP2179 from L. plantarum. (a) Stereo ribbon diagram of the LP2179 monomer color-coded from the N-terminus (blue) to the C-terminus (red). Helices
H1–H3 and ?-strands (?1–?7) are indicated. (b) Diagram showing the secondary-structure elements of LP2179 superimposed on its primary sequence. The labeling of
secondary-structure elements is in accord with PDBsum (http://www.ebi.ac.uk/pdbsum), where ?-helices are sequentially labeled (H1, H2, H3 etc), ?-strands are labeled
(A, B, C etc.) according to the ?-sheets to which they are assigned, ?-turns and ?-turns are designated by Greek letters (?, ?) and ?-hairpins by red loops. For LP2179, the
?-helices (H1–H3), ?-sheets (A, B) and ?-turns (?) are indicated. Selenomethionine residues used for phasing are labeled MSE.
sequence identity is only 7%. Similar values are obtained for
GK1089, another YugN homolog from Geobacillus kaustophilus
(PDB code 2r5x), with an r.m.s.d. of 2.9 A˚and 10% sequence identity
over 87 aligned residues. Both YugN-like homologs show an inter-
ruption in the regular hydrogen-bonding pattern of strand ?6 in the
?-sheet, resulting in two shorter, collinear strands that hydrogen
bond separately to ?5. However, as the TBP-like fold is characterized
by a ?-?-?4-? topology, the main topological difference between the
two families involves the first ?-sheet in LP2179, which is replaced in
YugN-like homologs by a ?-strand that forms part of the single
?-sheet (Fig. 2a). The H2 helix, which is absent in both YugN-like and
DUF1885 homologs, might constitute an additional difference, but
owing to its short size (one helical turn) and its involvement in crystal
contacts (Asp88–Arg1070and Phe85–Arg1070) it might not represent
a biologically relevant conformation of this region in solution.
Asearch with FFAS (Jaroszewski et al., 2005) showed nosignificant
sequence similarity of LP2179 to any protein family other than
PF08866. However, significant sequence similarity (FFAS score ?11
with 20% sequence identity) was observed between ABC2387 and
RBSTP2229, a member of the protein family PF08968 (DUF1885)
RBSTP2229 also exhibits a TBP-like fold. A structural superposition
of ABC2387 (PDB code 2pww) with RBSTP2229 (PDB code 1t6a)
shows a backbone r.m.s.d. of 2.8 A˚over 57 residues. Over the same
residue range, LP2179 has a backbone r.m.s.d. of 3.3 A˚
RBSTP2229 (Fig. 2b). However, the length and orientation of helix
Bakolitsa et al.
Acta Cryst. (2010). F66, 1205–1210
LP2179 exhibits structural similarity tomembers of the YugN-like family, DUF1185 and S-adenosylmethionine decarboxylases. Stereoviews of the structural superposition of
LP2179 (PDB code 2iay, in blue) with (in gray) (a) a YugN-like homolog from B. clausii (PDB code 2pww), (b) a DUF1885 homolog from B. stearothermophilus (PDB code
1t6a) and (c) S-adenosylmethionine decarboxylase proenzyme (TM0655) from Thermotoga maritima (PDB code 1vr7). N- and C-termini are indicated for LP2179 and are
indicated with primes (N0, C0) for other structures.
H1 in RBSTP2229 (pointing outwards from the structure instead of
packing against the central ?-sheet) differs substantially from that
observed in ABC2387 and LP2179, while the subsequent ?-strand is
positioned differently with respect to helix H3 in all three structures
(Figs. 2a and 2b). Among these TBP-like variants, LP2179 is unique in
that the N- and C-terminal ?-strands are combined to form an
additional ?-sheet that is situated between the central ?-sheet and
helix H3. However, both YugN-like and DUF1885 homologs display
shorter variants of this secondary-structure element in the same
region (YugN-like homologs contain a single ?-strand; DUF1185
forms a C-terminal hairpin), raising the possibility that this region
might represent a locus in this family for structural and possibly
functional drift (Krishna & Grishin, 2005).
Structural similarities of LP2179 to prokaryotic S-adenosyl-
methionine decarboxylases (AdoMetDCs; EC 184.108.40.206) were also
observed. Superposition of LP2179 onto the AdoMetDC from
Thermotoga maritima results in a backbone r.m.s.d. of 3.3 A˚over 82
residues with 3% sequence identity (Fig. 2c). Similar values (an
r.m.s.d of 3.3 A˚over 67 residues with 3% sequence identity) were
obtained for the AdoMetDC from Aquifex aeolicus (PDB code 2iii).
As with the YugN-like homologs, prokaryotic AdoMetDCs share a
similar fold and topology as LP2179 that includes the main ?-sheet
(?3–?6) and helices (H1–H3) in addition to the C-terminal ?-strand
(?7) of LP2179. The main differences involve the arrangement of the
N- and C-terminal ?-strands in prokaryotic AdoMetDCs that
hydrogen bond to form a single six-stranded antiparallel ?-sheet, as
opposed to the two separate sheets in LP2179, and a C-terminal helix
that is absent in LP2179 (Fig. 2c).
Structural comparison between these four Pfam families reveals
the conservation of a core ?-?-?4-? (TBP-like) fold with ?-strand
additions at the N- or C-terminus or both. In LP2179, a strand is
added at both the N- and C-termini, while YugN-like homologs
contain an extra ?-strand at the N-terminus (topology ?2-?-?4-?) and
PF08968 homologs contain an additional ?-strand at the C-terminus
that follows a circular permutation of the core fold (topology ?-?4-?-
?2). AdoMetDCs contain an additional ?-strand at the C-terminus
that hydrogen bonds to the N-terminal strand to form an antiparallel
six-stranded ?-sheet (topology ?-?-?4-?-?).
It is widely accepted that protein structure is more conserved than
between proteins might provide information that is not available
from sequence alone (see review by Kolodny et al., 2006). Both the
PF08866 (DUF1831) and PF08868 (YugN-like) protein families are
currently functionally uncharacterized. AdoMetDC is a pyruvoyl-
dependent amino-acid decarboxylase that is involved in methionine
metabolism and is essential for polyamine biosynthesis (Pegg et al.,
1998). The structure of prokaryotic AdoMetDC proenzyme (Toms et
al., 2004) reveals that despite the lack of any detectable sequence
similarity between the eukaryotic and prokaryotic forms of the
enzyme (13% sequence identity), the two structures can be super-
imposed with an r.m.s.d. of 2.0 A˚for 156 backbone residues. The
catalytic site residues are also conserved (Toms et al., 2004).
The AdoMetDC proenzyme undergoes an autocatalytic intra-
molecular self-cleavage reaction that generates a pyruvoyl group in a
loop between two ?-strands (?3 and ?4 in Fig. 2c). Although the
catalytic residues (Ser and Glu) of the AdoMetDC proenzyme are
not conserved in LP2179 and YugN-like or Pfam08968 homologs,
sequence alignment reveals the conservation of charged and aromatic
residue clusters between LP2179 and YugN-like homologs (Fig. 3). In
the respective structures, these clusters occur along the first two
strands and intervening loop of the central ?-sheet (?3 and ?4 in
Figs. 1a and 2c) surrounding the AdoMetDC catalytic site and may
serve a similar functional role.
3.3. Genomic neighborhood analysis
The genomic neighborhood (http://string.embl.de) of LP2179
shows a high degree of confidence in a predicted functional
association with cysteine desulfurase (LP2180, score 0.81) and
methylthioadenosine nucleosidase (LP2181, score 0.64). Cysteine
desulfurase (EC 220.127.116.11) catalyzes the production of alanine from
cysteine, while methylthioadenosine nucleosidase (EC 18.104.22.168) also
participates in the metabolism of amino groups. These two enzymes
are found in the genomic context or neighborhood of every member
of the DUF1831 family, supporting a role for DUF1831 in amino-acid
In Gram-positive bacteria, such as the Bacillus genus, amino-acid
metabolism is directly coupled to several other metabolic pathways,
including trans-sulfuration, polyamine synthesis and recycling, the
activated methyl cycle and quorum sensing (Lebeer et al., 2007). As
previously indicated, AdoMetDC is a central regulator of these
pathways. Modified amino acids, such as homocysteine, or their
catabolic products, such as polyamines, can serve both pathogenic
and probiotic roles. In pathogenic bacteria, polyamines and homo-
cysteine are involved in biofilm formation (Shah & Swiatlo, 2008;
Abraham, 2006), with polyamines also being implicated in bacterio-
cin production and protection from acid and oxidative stress (Shah &
Swiatlo, 2008). The probiotic role of lactobacilli has been well
documented (Ryan et al., 2008); their antimicrobial activity results
from the production of bacteriocins and antifungal peptides (De
Vuyst & Leroy, 2007). Further work will be required to determine
whether the fold similarities observed between the Bacillus protein
families described in this paper translate into similarities in function
and whether this function might involve a probiotic role.
The availability of more DUF1831 sequences and structures might
shed light on the evolutionary history of this intriguing protein family.
Acta Cryst. (2010). F66, 1205–1210Bakolitsa et al.
Sequence alignment of LP2179 and members of the YugN-like family. UniProt abbreviations are as follows: Q88V95_LACPL, gene locus lp_2179 from L. plantarum;
Q5WFD8_BACSK, gene locus ABC2387 from B. clausii; Q5L106_GEOKA, gene locus GK1089 from G. kaustophilus. Residues are shaded by identity (black) and similarity
The information presented here, in combination with further
biochemical and biophysical studies, should yield valuable in-
sights into the functional role of LP2179. Models for LP2179
homologs can be accessed at http://www1.jcsg.org/cgi-bin/models/
Additional information about the protein described in this study is
available from TOPSAN (Krishna et al., 2010) http://www.topsan.org/
The first structural representative of the DUF1831 family reveals a
potential new fold with remote similarities to TBP-like structures.
This similarity, in combination with genomic context analysis, leads us
to propose an involvement in amino-acid metabolism that might also
be extended to two other families of unknown function.
This work was supported by the National Institute of General
Medical Sciences Protein Structure Initiative grant Nos. P50
GM62411 and U54 GM074898. Portions of this research were carried
out at the APS beamline 23-ID-D of GM/CA-CAT, the ALS beam-
line 8.2.2 of BCSB and Stanford Synchrotron Radiation Lightsource
(SSRL). Use of the Advanced Photon Source was supported by the
US Department of Energy, Office of Science, Office of Basic Energy
Sciences under Contract No. DE-AC02-06CH11357. GM/CA CAT
has been funded in whole or in part with Federal funds from the
National Cancer Institute (Y1-CO-1020) and the National Institute of
General Medical Science (Y1-GM-1104). The Advanced Light
Source is supported by the Director, Office of Science, Office of Basic
Energy Sciences of the US Department of Energy under Contract
No. DE-AC02-05CH11231. The Berkeley Center for Structural
Biology is supported in part by the National Institutes of Health,
National Institute of General Medical Sciences. The SSRL is a
national user facility operated by Stanford University on behalf ofthe
US Department of Energy, Office of Basic Energy Sciences. The
SSRL Structural Molecular Biology Program is supported by the
Department of Energy, Office of Biological and Environmental
Research and by the National Institutes of Health (National Center
for Research Resources, Biomedical Technology Program and the
National Institute of General Medical Sciences). The content is solely
the responsibility of the authors and does not necessarily represent
the official views of the National Institute of General Medical
Sciences or the National Institutes of Health. Genomic DNA from
L. plantarum WCFS1 NCIMB8826 (ATCC No. BAA-793D) was
obtained from the American Type Culture Collection (ATCC).
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