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PDBsum entry 1chm

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protein ligands Protein-protein interface(s) links
Creatinase PDB id
1chm
Jmol
Contents
Protein chains
401 a.a. *
Ligands
CMS ×2
Waters ×394
* Residue conservation analysis
PDB id:
1chm
Name: Creatinase
Title: Enzymatic mechanism of creatine amidinohydrolase as deduced from crystal structures
Structure: Creatine amidinohydrolase. Chain: a, b. Engineered: yes
Source: Pseudomonas putida. Organism_taxid: 303
Biol. unit: Dimer (from PQS)
Resolution:
1.90Å     R-factor:   0.177    
Authors: H.W.Hoeffken,S.H.Knof,P.A.Bartlett,R.Huber,H.Moellering, G.Schumacher
Key ref: M.Coll et al. (1990). Enzymatic mechanism of creatine amidinohydrolase as deduced from crystal structures. J Mol Biol, 214, 597-610. PubMed id: 1696320
Date:
19-Jul-93     Release date:   30-Apr-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P38488  (CREA_PSEPU) -  Creatinase
Seq:
Struc:
403 a.a.
401 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.5.3.3  - Creatinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Creatine Biosynthesis
      Reaction: Creatine + H2O = sarcosine + urea
Creatine
Bound ligand (Het Group name = CMS)
matches with 80.00% similarity
+ H(2)O
= sarcosine
+ urea
      Cofactor: Mn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     hydrolase activity     2 terms  

 

 
    reference    
 
 
J Mol Biol 214:597-610 (1990)
PubMed id: 1696320  
 
 
Enzymatic mechanism of creatine amidinohydrolase as deduced from crystal structures.
M.Coll, S.H.Knof, Y.Ohga, A.Messerschmidt, R.Huber, H.Moellering, L.Rüssmann, G.Schumacher.
 
  ABSTRACT  
 
Crystal structures of the enzyme creatine amidinohydrolase (creatinase, EC 3.5.3.3) with two different inhibitors, the reaction product sarcosine and the substrate creatine, bound have been analyzed by X-ray diffraction methods. With the inhibitor carbamoyl sarcosine, two different crystal forms at different pH values have been determined. An enzymatic mechanism is proposed on the basis of the eight structures analyzed. The enzyme binds substrate and inhibitor in a distorted geometry where the urea resonance is broken. His232 is the general base and acid, and acts as a proton shuttle. It withdraws a proton from water 377 and donates it to the N(3) atom of the guanidinium group. OH- 377 adds to the C(1) atom of the guanidinium group to form a urea hydrate. Proton withdrawal by His232 leads to products. The reaction product sarcosine binds to the active site in a reverse orientation. The free enzyme was found to have a bicarbonate bound to the active site.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18089575 A.P.VanDemark, H.Xin, L.McCullough, R.Rawlins, S.Bentley, A.Heroux, D.J.Stillman, C.P.Hill, and T.Formosa (2008).
Structural and functional analysis of the Spt16p N-terminal domain reveals overlapping roles of yFACT subunits.
  J Biol Chem, 283, 5058-5068.
PDB codes: 3bip 3biq 3bit
18579787 T.Stuwe, M.Hothorn, E.Lejeune, V.Rybin, M.Bortfeld, K.Scheffzek, and A.G.Ladurner (2008).
The FACT Spt16 "peptidase" domain is a histone H3-H4 binding module.
  Proc Natl Acad Sci U S A, 105, 8884-8889.
PDB codes: 3cb5 3cb6
17221239 A.Ramanavicius (2007).
Amperometric biosensor for the determination of creatine.
  Anal Bioanal Chem, 387, 1899-1906.  
16784220 M.W.Clarkson, S.A.Gilmore, M.H.Edgell, and A.L.Lee (2006).
Dynamic coupling and allosteric behavior in a nonallosteric protein.
  Biochemistry, 45, 7693-7699.  
12136144 B.Padmanabhan, A.Paehler, and M.Horikoshi (2002).
Structure of creatine amidinohydrolase from Actinobacillus.
  Acta Crystallogr D Biol Crystallogr, 58, 1322-1328.
PDB code: 1kp0
11807264 B.Padmanabhan, and M.Horikoshi (2002).
Crystallization and preliminary X-ray diffraction analysis of creatine amidinohydrolase from Actinobacillus.
  Acta Crystallogr D Biol Crystallogr, 58, 322-323.  
12400161 K.Ito (2002).
[Structural and functional analysis of enzymes and their application to clinical analysis--study on Pseudomonas putida formaldehyde dehydrogenase]
  Yakugaku Zasshi, 122, 805-811.  
10944393 H.Ponstingl, K.Henrick, and J.M.Thornton (2000).
Discriminating between homodimeric and monomeric proteins in the crystalline state.
  Proteins, 41, 47-57.  
  9797327 J.Matos, M.Nardi, H.Kumura, and V.Monnet (1998).
Genetic characterization of pepP, which encodes an aminopeptidase P whose deficiency does not affect Lactococcus lactis growth in milk, unlike deficiency of the X-prolyl dipeptidyl aminopeptidase.
  Appl Environ Microbiol, 64, 4591-4595.  
9507056 J.Perozich, J.Hempel, and S.M.Morris (1998).
Roles of conserved residues in the arginase family.
  Biochim Biophys Acta, 1382, 23-37.  
9520390 M.C.Wilce, C.S.Bond, N.E.Dixon, H.C.Freeman, J.M.Guss, P.E.Lilley, and J.A.Wilce (1998).
Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli.
  Proc Natl Acad Sci U S A, 95, 3472-3477.
PDB codes: 1a16 1az9 1jaw
9218780 A.Humm, E.Fritsche, S.Steinbacher, and R.Huber (1997).
Crystal structure and mechanism of human L-arginine:glycine amidinotransferase: a mitochondrial enzyme involved in creatine biosynthesis.
  EMBO J, 16, 3373-3385.
PDB codes: 1jdw 2jdw 3jdw 4jdw
  9165062 W.Baumeister, Z.Cejka, M.Kania, and E.Seemüller (1997).
The proteasome: a macromolecular assembly designed to confine proteolysis to a nanocompartment.
  Biol Chem, 378, 121-130.  
7816812 M.Egli, and R.V.Gessner (1995).
Stereoelectronic effects of deoxyribose O4' on DNA conformation.
  Proc Natl Acad Sci U S A, 92, 180-184.  
8041800 H.Kubinyi (1994).
[The key and the lock. I. The basis of drug action]
  Pharm Unserer Zeit, 23, 158-168.  
8146141 J.F.Bazan, L.H.Weaver, S.L.Roderick, R.Huber, and B.W.Matthews (1994).
Sequence and structure comparison suggest that methionine aminopeptidase, prolidase, aminopeptidase P, and creatinase share a common fold.
  Proc Natl Acad Sci U S A, 91, 2473-2477.  
8291080 A.G.Murzin (1993).
Can homologous proteins evolve different enzymatic activities?
  Trends Biochem Sci, 18, 403-405.  
  8251936 J.Schumann, G.Böhm, G.Schumacher, R.Rudolph, and R.Jaenicke (1993).
Stabilization of creatinase from Pseudomonas putida by random mutagenesis.
  Protein Sci, 2, 1612-1620.  
8504814 J.Schumann, and R.Jaenicke (1993).
Creatinase in its collapsed A state shows properties of a molten globule with dimeric quaternary structure.
  Eur J Biochem, 213, 1225-1233.  
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.