Structural basis of murein peptide specificity of a gamma-D-glutamyl-l-diamino acid endopeptidase.
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.
Xu
Qingping
Q
Joint Center for Structural Genomics, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.
Sudek
Sebastian
S
McMullan
Daniel
D
Miller
Mitchell D
MD
Geierstanger
Bernhard
B
Jones
David H
DH
Krishna
S Sri
SS
Spraggon
Glen
G
Bursalay
Badry
B
Abdubek
Polat
P
Acosta
Claire
C
Ambing
Eileen
E
Astakhova
Tamara
T
Axelrod
Herbert L
HL
Carlton
Dennis
D
Caruthers
Jonathan
J
Chiu
Hsiu-Ju
HJ
Clayton
Thomas
T
Deller
Marc C
MC
Duan
Lian
L
Elias
Ylva
Y
Elsliger
Marc-André
MA
Feuerhelm
Julie
J
Grzechnik
Slawomir K
SK
Hale
Joanna
J
Han
Gye Won
GW
Haugen
Justin
J
Jaroszewski
Lukasz
L
Jin
Kevin K
KK
Klock
Heath E
HE
Knuth
Mark W
MW
Kozbial
Piotr
P
Kumar
Abhinav
A
Marciano
David
D
Morse
Andrew T
AT
Nigoghossian
Edward
E
Okach
Linda
L
Oommachen
Silvya
S
Paulsen
Jessica
J
Reyes
Ron
R
Rife
Christopher L
CL
Trout
Christina V
CV
van den Bedem
Henry
H
Weekes
Dana
D
White
Aprilfawn
A
Wolf
Guenter
G
Zubieta
Chloe
C
Hodgson
Keith O
KO
Wooley
John
J
Deacon
Ashley M
AM
Godzik
Adam
A
Lesley
Scott A
SA
Wilson
Ian A
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D000595:Amino Acid Sequence; D046870:Anabaena variabilis / Q000737:chemistry / Q000201:enzymology; D020134:Catalytic Domain; D003546:Cysteine Endopeptidases / Q000737:chemistry / Q000378:metabolism / Q000502:physiology; D010450:Endopeptidases / Q000737:chemistry* / Q000378:metabolism* / Q000502:physiology; D008954:Models, Biological; D008958:Models, Molecular; D008969:Molecular Sequence Data; D046937:Nostoc / Q000737:chemistry / Q000201:enzymology; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism; D010457:Peptidoglycan / Q000737:chemistry* / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity; D018909:src Homology Domains
D010446:Peptide Fragments; D010457:Peptidoglycan; D010450:Endopeptidases; D003546:Cysteine Endopeptidases; C038279:gamma-D-glutamyl-L-diaminoacid endopeptidase