Sebastian Sudek

Publications (2)9.74 Total impact

• Article: Structural basis of murein peptide specificity of a gamma-D-glutamyl-l-diamino acid endopeptidase.

  Qingping Xu, Sebastian Sudek, Daniel McMullan, Mitchell D Miller, Bernhard Geierstanger, David H Jones, S Sri Krishna, Glen Spraggon, Badry Bursalay, Polat Abdubek, [......], Dana Weekes, Aprilfawn White, Guenter Wolf, Chloe Zubieta, Keith O Hodgson, John Wooley, Ashley M Deacon, Adam Godzik, Scott A Lesley, Ian A Wilson
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  ABSTRACT: The crystal structures of two homologous endopeptidases from cyanobacteria Anabaena variabilis and Nostoc punctiforme were determined at 1.05 and 1.60 A resolution, respectively, and contain a bacterial SH3-like domain (SH3b) and a ubiquitous cell-wall-associated NlpC/P60 (or CHAP) cysteine peptidase domain. The NlpC/P60 domain is a primitive, papain-like peptidase in the CA clan of cysteine peptidases with a Cys126/His176/His188 catalytic triad and a conserved catalytic core. We deduced from structure and sequence analysis, and then experimentally, that these two proteins act as gamma-D-glutamyl-L-diamino acid endopeptidases (EC 3.4.22.-). The active site is located near the interface between the SH3b and NlpC/P60 domains, where the SH3b domain may help define substrate specificity, instead of functioning as a targeting domain, so that only muropeptides with an N-terminal L-alanine can bind to the active site.
  Structure 03/2009; 17(2):303-13. · 6.35 Impact Factor
• Article: Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution.

  Debanu Das, Piotr Kozbial, Herbert L Axelrod, Mitchell D Miller, Daniel McMullan, S Sri Krishna, Polat Abdubek, Claire Acosta, Tamara Astakhova, Prasad Burra, [......], Henry van den Bedem, Dana Weekes, Aprilfawn White, Qingping Xu, Keith O Hodgson, John Wooley, Ashley M Deacon, Adam Godzik, Scott A Lesley, Ian A Wilson
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  ABSTRACT: ECX21941 represents a very large family (over 600 members) of novel, ocean metagenome-specific proteins identified by clustering of the dataset from the Global Ocean Sampling expedition. The crystal structure of ECX21941 reveals unexpected similarity to Sm/LSm proteins, which are important RNA-binding proteins, despite no detectable sequence similarity. The ECX21941 protein assembles as a homopentamer in solution and in the crystal structure when expressed in Escherichia coli and represents the first pentameric structure for this Sm/LSm family of proteins, although the actual oligomeric form in vivo is currently not known. The genomic neighborhood analysis of ECX21941 and its homologs combined with sequence similarity searches suggest a cyanophage origin for this protein. The specific functions of members of this family are unknown, but our structure analysis of ECX21941 indicates nucleic acid-binding capabilities and suggests a role in RNA and/or DNA processing.
  Proteins Structure Function and Bioinformatics 01/2009; 75(2):296-307. · 3.39 Impact Factor