1CHM | pdb_00001chm

ENZYMATIC MECHANISM OF CREATINE AMIDINOHYDROLASE AS DEDUCED FROM CRYSTAL STRUCTURES

• PDB DOI: https://doi.org/10.2210/pdb1CHM/pdb

• Classification: CREATINASE
• Organism(s): Pseudomonas putida
• Mutation(s): No 


• Deposited: 1993-07-19 Released: 1994-04-30 
• Deposition Author(s): Hoeffken, H.W., Knof, S.H., Bartlett, P.A., Huber, R., Moellering, H., Schumacher, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Work: 
  0.177 (Depositor) 

Literature

Enzymatic mechanism of creatine amidinohydrolase as deduced from crystal structures.

Coll, M., Knof, S.H., Ohga, Y., Messerschmidt, A., Huber, R., Moellering, H., Russmann, L., Schumacher, G.

(1990) J Mol Biology 214: 597-610

• PubMed: 1696320 
• DOI: https://doi.org/10.1016/0022-2836(90)90201-v
• Primary Citation Related Structures: 
  1CHM


• PubMed 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.

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Organizational Affiliation: 
• Max-Planck-Institut fuer Biochemie, Martinsried bei Muenchen, F.R.G.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 90.93 kDa 
• Atom Count: 6,786 
• Modeled Residue Count: 802 
• Deposited Residue Count: 802 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CREATINE AMIDINOHYDROLASE	A, B	401	Pseudomonas putida	Mutation(s): 0  EC: 3.5.3.3
UniProt
Find proteins for P38488 (Pseudomonas putida) Explore P38488  Go to UniProtKB:  P38488

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CMS	C [auth A], D [auth B]	CARBAMOYL SARCOSINE C4 H8 N2 O3 SREKYKXYSQMOIB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Work:  0.177 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.83	α = 90
b = 110.55	β = 102.22
c = 62.63	γ = 90

Software Package:

Software Name	Purpose
EREF	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-04-30 
Deposition Author(s): Hoeffken, H.W., Knof, S.H., Bartlett, P.A., Huber, R., Moellering, H., Schumacher, G.

Revision History  

• Version 1.0: 1994-04-30
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other