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PDBsum entry 3s8r

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
3s8r
Jmol
Contents
Protein chains
684 a.a.
Ligands
GOL ×2
Waters ×878
PDB id:
3s8r
Name: Hydrolase
Title: Crystal structures of glutaryl 7-aminocephalosporanic acid a insight into autoproteolytic activation
Structure: Glutaryl-7-aminocephalosporanic-acid acylase. Chain: a, b. Synonym: glutaryl-7-aca acylase, 7-beta-(4-carboxybutanamid cephalosporanic acid acylase, gl-7-aca acylase, gca, glutar aminocephalosporanic-acid acylase subunit alpha, glutaryl-7 acylase subunit alpha, glutaryl-7-aminocephalosporanic-acid subunit beta, glutaryl-7-aca acylase subunit beta. Engineered: yes. Mutation: yes
Source: Pseudomonas. Organism_taxid: 269086. Strain: sy-77-1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.50Å     R-factor:   0.156     R-free:   0.200
Authors: J.K.Kim,I.S.Yang,S.S.Park,K.H.Kim
Key ref:
J.K.Kim et al. (2003). Crystal structures of glutaryl 7-aminocephalosporanic acid acylase: insight into autoproteolytic activation. Biochemistry, 42, 4084-4093. PubMed id: 12680762 DOI: 10.1021/bi027181x
Date:
30-May-11     Release date:   06-Jul-11    
Supersedes: 1oqz
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P07662  (G7AC_PSEU7) -  Glutaryl-7-aminocephalosporanic-acid acylase
Seq:
Struc:
 
Seq:
Struc:
720 a.a.
684 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.5.1.93  - Glutaryl-7-aminocephalosporanic-acid acylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (7R)-7-(4-carboxybutanamido)cephalosporanate + H2O = (7R)-7- aminocephalosporanate + glutarate
(7R)-7-(4-carboxybutanamido)cephalosporanate
+ H(2)O
= (7R)-7- aminocephalosporanate
+ glutarate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   1 term 
  Biological process     response to antibiotic   2 terms 
  Biochemical function     hydrolase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi027181x Biochemistry 42:4084-4093 (2003)
PubMed id: 12680762  
 
 
Crystal structures of glutaryl 7-aminocephalosporanic acid acylase: insight into autoproteolytic activation.
J.K.Kim, I.S.Yang, S.Rhee, Z.Dauter, Y.S.Lee, S.S.Park, K.H.Kim.
 
  ABSTRACT  
 
Glutaryl 7-aminocephalosporanic acid acylase (GCA, EC 3.5.1.11) is a member of N-terminal nucleophile (Ntn) hydrolases. The native enzyme is an (alpha beta)(2) heterotetramer originated from an enzymatically inactive precursor of a single polypeptide. The activation of precursor GCA consists of primary and secondary autoproteolytic cleavages, generating a terminal residue with both a nucleophile and a base and releasing a nine amino acid spacer peptide. We have determined the crystal structures of the recombinant selenomethionyl native and S170A mutant precursor from Pseudomonas sp. strain GK16. Precursor activation is likely triggered by conformational constraints within the spacer peptide, probably inducing a peptide flip. Autoproteolytic site solvent molecules, which have been trapped in a hydrophobic environment by the spacer peptide, may play a role as a general base for nucleophilic attack. The activation results in building up a catalytic triad composed of Ser170/His192/Glu624. However, the triad is not linked to the usual hydroxyl but the free alpha-amino group of the N-terminal serine residue of the native GCA. Mutagenesis and structural data support the notion that the stabilization of a transient hydroxazolidine ring during autoproteolysis would be critical during the N --> O acyl shift. The autoproteolytic activation mechanism for GCA is described.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20673217 H.P.Chang, W.C.Liang, R.C.Lyu, M.C.Chi, T.F.Wang, K.L.Su, H.C.Hung, and L.L.Lin (2010).
Effects of C-terminal truncation on autocatalytic processing of Bacillus licheniformis gamma-glutamyl transpeptidase.
  Biochemistry (Mosc), 75, 919-929.  
19706171 K.Lakomek, A.Dickmanns, M.Kettwig, H.Urlaub, R.Ficner, and T.Lübke (2009).
Initial insight into the function of the lysosomal 66.3 kDa protein from mouse by means of X-ray crystallography.
  BMC Struct Biol, 9, 56.
PDB codes: 3fgr 3fgt 3fgw
18334484 K.Michalska, A.Hernandez-Santoyo, and M.Jaskolski (2008).
The mechanism of autocatalytic activation of plant-type L-asparaginases.
  J Biol Chem, 283, 13388-13397.
PDB code: 3c17
17922842 L.G.Otten, C.F.Sio, C.R.Reis, G.Koch, R.H.Cool, and W.J.Quax (2007).
A highly active adipyl-cephalosporin acylase obtained via rational randomization.
  FEBS J, 274, 5600-5610.  
17157318 Y.Wang, and H.C.Guo (2007).
Crystallographic snapshot of a productive glycosylasparaginase-substrate complex.
  J Mol Biol, 366, 82-92.
PDB code: 2gl9
16495538 C.F.Sio, L.G.Otten, R.H.Cool, S.P.Diggle, P.G.Braun, R.Bos, M.Daykin, M.Cámara, P.Williams, and W.J.Quax (2006).
Quorum quenching by an N-acyl-homoserine lactone acylase from Pseudomonas aeruginosa PAO1.
  Infect Immun, 74, 1673-1682.  
16446446 J.K.Kim, I.S.Yang, H.J.Shin, K.J.Cho, E.K.Ryu, S.H.Kim, S.S.Park, and K.H.Kim (2006).
Insight into autoproteolytic activation from the structure of cephalosporin acylase: a protein with two proteolytic chemistries.
  Proc Natl Acad Sci U S A, 103, 1732-1737.
PDB codes: 2adv 2ae3 2ae4 2ae5
16850301 L.L.Lin, P.R.Chou, Y.W.Hua, and W.H.Hsu (2006).
Overexpression, one-step purification, and biochemical characterization of a recombinant gamma-glutamyltranspeptidase from Bacillus licheniformis.
  Appl Microbiol Biotechnol, 73, 103-112.  
15946951 K.Michalska, K.Brzezinski, and M.Jaskolski (2005).
Crystal structure of isoaspartyl aminopeptidase in complex with L-aspartate.
  J Biol Chem, 280, 28484-28491.
PDB codes: 1seo 2zal
  16508111 P.M.Chandra, J.A.Brannigan, A.Prabhune, A.Pundle, J.P.Turkenburg, G.G.Dodson, and C.G.Suresh (2005).
Cloning, preparation and preliminary crystallographic studies of penicillin V acylase autoproteolytic processing mutants.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 124-127.
PDB code: 2iwm
15221226 K.Nagao, M.Yamashita, and M.Ueda (2004).
Production of autoproteolytically subunit-assembled 7-beta-(4-carboxybutanamido)cephalosporanic acid (GL-7ACA) acylase from Pseudomonas sp. C427 using a chitin-binding domain.
  Appl Microbiol Biotechnol, 65, 407-413.  
15174165 L.G.Otten, C.F.Sio, A.M.van der Sloot, R.H.Cool, and W.J.Quax (2004).
Mutational analysis of a key residue in the substrate specificity of a cephalosporin acylase.
  Chembiochem, 5, 820-825.  
14633979 F.Schmitzberger, M.L.Kilkenny, C.M.Lobley, M.E.Webb, M.Vinkovic, D.Matak-Vinkovic, M.Witty, D.Y.Chirgadze, A.G.Smith, C.Abell, and T.L.Blundell (2003).
Structural constraints on protein self-processing in L-aspartate-alpha-decarboxylase.
  EMBO J, 22, 6193-6204.
PDB codes: 1ppy 1pqe 1pqf 1pqh 1pt0 1pt1 1pyq 1pyu
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.