ISDA

Deposition Date 2005-12-20

Release Date 2006-01-10

Last Version Date 2024-11-13

Entry Detail

PDB ID:

2FG0

Keywords:

HYDROLASE

Title:

Crystal structure of a putative gamma-d-glutamyl-l-diamino acid endopeptidase (npun_r0659) from nostoc punctiforme pcc 73102 at 1.79 A resolution

Biological Source:

Source Organism:

Nostoc punctiforme (Taxon ID: 63737)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.79 Å

R-Value Free:

0.17

R-Value Work:

0.15

Space Group:

P 41 21 2

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:COG0791: Cell wall-associated hydrolases (invasion-associated proteins)
Chain IDs:A, B
Chain Length:246
Number of Molecules:2
Biological Source:Nostoc punctiforme

UniProt ID:B2J9B4 Pfam ID:PF18348, PF00877

Modified Residue

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

Ligand Molecules

GOL

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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Disease

Primary Citation of related structures