3H41

CRYSTAL STRUCTURE OF A NLPC/P60 FAMILY PROTEIN (BCE_2878) FROM BACILLUS CEREUS ATCC 10987 AT 1.79 A RESOLUTION

3H41 の概要

• エントリーDOI: 10.2210/pdb3h41/pdb
• 分子名称: NLP/P60 family protein, ALANINE, D-GLUTAMIC ACID, ... (6 entities in total)
• 機能のキーワード: nlpc/p60 family protein, structural genomics, joint center for structural genomics, jcsg, protein structure initiative, psi-2, hydrolase
• 由来する生物種: Bacillus cereus ATCC 10987
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 36665.32

構造登録者

Joint Center for Structural Genomics (JCSG) (登録日: 2009-04-17, 公開日: 2009-05-05, 最終更新日: 2023-02-01)

主引用文献

Xu, Q.,Abdubek, P.,Astakhova, T.,Axelrod, H.L.,Bakolitsa, C.,Cai, X.,Carlton, D.,Chen, C.,Chiu, H.J.,Chiu, M.,Clayton, T.,Das, D.,Deller, M.C.,Duan, L.,Ellrott, K.,Farr, C.L.,Feuerhelm, J.,Grant, J.C.,Grzechnik, A.,Han, G.W.,Jaroszewski, L.,Jin, K.K.,Klock, H.E.,Knuth, M.W.,Kozbial, P.,Krishna, S.S.,Kumar, A.,Lam, W.W.,Marciano, D.,Miller, M.D.,Morse, A.T.,Nigoghossian, E.,Nopakun, A.,Okach, L.,Puckett, C.,Reyes, R.,Tien, H.J.,Trame, C.B.,van den Bedem, H.,Weekes, D.,Wooten, T.,Yeh, A.,Hodgson, K.O.,Wooley, J.,Elsliger, M.A.,Deacon, A.M.,Godzik, A.,Lesley, S.A.,Wilson, I.A.
Structure of the gamma-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-[gamma]-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases
Acta Crystallogr.,Sect.F, 66:1354-1364, 2010

PubMed Abstract: Dipeptidyl-peptidase VI from Bacillus sphaericus and YkfC from Bacillus subtilis have both previously been characterized as highly specific γ-D-glutamyl-L-diamino acid endopeptidases. The crystal structure of a YkfC ortholog from Bacillus cereus (BcYkfC) at 1.8 Å resolution revealed that it contains two N-terminal bacterial SH3 (SH3b) domains in addition to the C-terminal catalytic NlpC/P60 domain that is ubiquitous in the very large family of cell-wall-related cysteine peptidases. A bound reaction product (L-Ala-γ-D-Glu) enabled the identification of conserved sequence and structural signatures for recognition of L-Ala and γ-D-Glu and, therefore, provides a clear framework for understanding the substrate specificity observed in dipeptidyl-peptidase VI, YkfC and other NlpC/P60 domains in general. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed. A conserved tyrosine in the SH3b domain of the YkfC subfamily is correlated with the presence of a conserved acidic residue in the NlpC/P60 domain and both residues interact with the free amine group of the alanine. This structural feature allows the definition of a subfamily of NlpC/P60 enzymes with the same N-terminal substrate requirements, including a previously characterized cyanobacterial L-alanine-γ-D-glutamate endopeptidase that contains the two key components (an NlpC/P60 domain attached to an SH3b domain) for assembly of a YkfC-like active site.

PubMed: 20944232
DOI: 10.1107/S1744309110021214

実験手法

X-RAY DIFFRACTION (1.79 Å)