2HBW

Crystal structure of a putative endopeptidase (ava_3396) from anabaena variabilis atcc 29413 at 1.05 A resolution

Summary for 2HBW

• Entry DOI: 10.2210/pdb2hbw/pdb
• Descriptor: NLP/P60 protein, ACETATE ION, UNKNOWN LIGAND, ... (4 entities in total)
• Functional Keywords: nlp/p60 family protein, structural genomics, joint center for structural genomics, jcsg, protein structure initiative, psi-2, hydrolase
• Biological source: Anabaena variabilis
• Total number of polymer chains: 1
• Total formula weight: 25651.33

Authors

Joint Center for Structural Genomics (JCSG) (deposition date: 2006-06-14, release date: 2006-08-08, Last modification date: 2024-11-20)

Primary citation

Xu, Q.,Sudek, S.,McMullan, D.,Miller, M.D.,Geierstanger, B.,Jones, D.H.,Krishna, S.S.,Spraggon, G.,Bursalay, B.,Abdubek, P.,Acosta, C.,Ambing, E.,Astakhova, T.,Axelrod, H.L.,Carlton, D.,Caruthers, J.,Chiu, H.J.,Clayton, T.,Deller, M.C.,Duan, L.,Elias, Y.,Elsliger, M.A.,Feuerhelm, J.,Grzechnik, S.K.,Hale, J.,Won Han, G.,Haugen, J.,Jaroszewski, L.,Jin, K.K.,Klock, H.E.,Knuth, M.W.,Kozbial, P.,Kumar, A.,Marciano, D.,Morse, A.T.,Nigoghossian, E.,Okach, L.,Oommachen, S.,Paulsen, J.,Reyes, R.,Rife, C.L.,Trout, C.V.,van den Bedem, H.,Weekes, D.,White, A.,Wolf, G.,Zubieta, C.,Hodgson, K.O.,Wooley, J.,Deacon, A.M.,Godzik, A.,Lesley, S.A.,Wilson, I.A.
Structural Basis of Murein Peptide Specificity of a gamma-D-Glutamyl-L-Diamino Acid Endopeptidase.
Structure, 17:303-313, 2009

PubMed 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.

PubMed: 19217401
DOI: 10.1016/j.str.2008.12.008

Experimental method

X-RAY DIFFRACTION (1.05 Å)