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PDBsum entry 1j2u

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1j2u
Jmol
Contents
Protein chains
(+ 0 more) 257 a.a. *
Ligands
SO4 ×10
Metals
_ZN ×12
Waters ×1315
* Residue conservation analysis
PDB id:
1j2u
Name: Hydrolase
Title: Creatininase zn
Structure: Creatinine amidohydrolase. Chain: a, b, c, d, e, f. Synonym: diagnase. Engineered: yes
Source: Pseudomonas putida. Organism_taxid: 303. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PQS)
Resolution:
1.85Å     R-factor:   0.187     R-free:   0.201
Authors: T.Yoshimoto,N.Tanaka,N.Kanada,T.Inoue,Y.Nakajima,M.Haratake, K.T.Nakamura,Y.Xu,K.Ito
Key ref:
T.Yoshimoto et al. (2004). Crystal structures of creatininase reveal the substrate binding site and provide an insight into the catalytic mechanism. J Mol Biol, 337, 399-416. PubMed id: 15003455 DOI: 10.1016/j.jmb.2004.01.022
Date:
11-Jan-03     Release date:   27-Jan-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P83772  (CRNA_PSEPU) -  Creatinine amidohydrolase
Seq:
Struc:
260 a.a.
257 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.5.2.10  - Creatininase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Creatinine + H2O = creatine
Creatinine
+ H(2)O
= creatine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     creatinine catabolic process   2 terms 
  Biochemical function     hydrolase activity     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/j.jmb.2004.01.022 J Mol Biol 337:399-416 (2004)
PubMed id: 15003455  
 
 
Crystal structures of creatininase reveal the substrate binding site and provide an insight into the catalytic mechanism.
T.Yoshimoto, N.Tanaka, N.Kanada, T.Inoue, Y.Nakajima, M.Haratake, K.T.Nakamura, Y.Xu, K.Ito.
 
  ABSTRACT  
 
Creatininase from Pseudomonas putida is a member of the urease-related amidohydrolase superfamily. The crystal structure of the Mn-activated enzyme has been solved by the single isomorphous replacement method at 1.8A resolution. The structures of the native creatininase and the Mn-activated creatininase-creatine complex have been determined by a difference Fourier method at 1.85 A and 1.6 A resolution, respectively. We found the disc-shaped hexamer to be roughly 100 A in diameter and 50 A in thickness and arranged as a trimer of dimers with 32 (D3) point group symmetry. The enzyme is a typical Zn2+ enzyme with a binuclear metal center (metal1 and metal2). Atomic absorption spectrometry and X-ray crystallography revealed that Zn2+ at metal1 (Zn1) was easily replaced with Mn2+ (Mn1). In the case of the Mn-activated enzyme, metal1 (Mn1) has a square-pyramidal geometry bound to three protein ligands of Glu34, Asp45, and His120 and two water molecules. Metal2 (Zn2) has a well-ordered tetrahedral geometry bound to the three protein ligands of His36, Asp45, and Glu183 and a water molecule. The crystal structure of the Mn-activated creatininase-creatine complex, which is the first structure as the enzyme-substrate/inhibitor complex of creatininase, reveals that significant conformation changes occur at the flap (between the alpha5 helix and the alpha6 helix) of the active site and the creatine is accommodated in a hydrophobic pocket consisting of Trp174, Trp154, Tyr121, Phe182, Tyr153, and Gly119. The high-resolution crystal structure of the creatininase-creatine complex enables us to identify two water molecules (Wat1 and Wat2) that are possibly essential for the catalytic mechanism of the enzyme. The structure and proposed catalytic mechanism of the creatininase are different from those of urease-related amidohydrolase superfamily enzymes. We propose a new two-step catalytic mechanism possibly common to creatininases in which the Wat1 acts as the attacking nucleophile in the water-adding step and the Wat2 acts as the catalytic acid in the ring-opening step.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Stereo diagrams showing the coordination of the binuclear metal center of creatininase. The distances from the metal ions to the ligands of the binuclear metal center of creatininase and those from the water molecules to its ligands are shown (in Å). (a) The Mn-activated creatininase. The Mn1 has a square-pyramidal geometry, whereas the Zn2 is revealed as having ordered tetrahedral geometry. (b) Native creatininase. The Zn1 has distorted tetrahedral geometry, whereas the Zn2 has ordered tetrahedral geometry.
Figure 9.
Figure 9. Proposed catalytic mechanism of creatininase.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 337, 399-416) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20803053 V.S.Lee, K.Kodchakorn, J.Jitonnom, P.Nimmanpipug, P.Kongtawelert, and B.Premanode (2010).
Influence of metal cofactors and water on the catalytic mechanism of creatininase-creatinine in aqueous solution from molecular dynamics simulation and quantum study.
  J Comput Aided Mol Des, 24, 879-886.  
17603262 T.Yoshimoto (2007).
[Biochemistry and structural biology of microbial enzymes and their medical applications]
  Yakugaku Zasshi, 127, 1035-1045.  
16470765 L.F.Huang, B.Su, S.C.Jao, K.T.Liu, and W.S.Li (2006).
Aminopeptidase p mediated detoxification of organophosphonate analogues of sarin: mechanistic and stereochemical study at the phosphorus atom of the substrate.
  Chembiochem, 7, 506-514.  
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.