ISDA

Deposition Date 2006-06-14

Release Date 2006-08-08

Last Version Date 2024-11-20

Entry Detail

PDB ID:

2HBW

Keywords:

HYDROLASE

Title:

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

Biological Source:

Source Organism:

Anabaena variabilis (Taxon ID: 240292)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.05 Å

R-Value Free:

0.14

R-Value Work:

0.12

R-Value Observed:

0.12

Space Group:

P 21 21 2

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:NLP/P60 protein
Gene (Uniprot):Ava_3396
Chain IDs:A
Chain Length:235
Number of Molecules:1
Biological Source:Anabaena variabilis

UniProt ID:Q3M7N3 Pfam ID:PF18348, PF00877

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
MSE	A	MET	SELENOMETHIONINE

Ligand Molecules

ACT

UNL

Primary Citation

Structural Basis of Murein Peptide Specificity of a gamma-D-Glutamyl-L-Diamino Acid Endopeptidase.

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.Show

Structure 17 303 313 (2009)

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

Abstact

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.

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Primary Citation of related structures