PDBsum entry 1v7z

Hydrolase

PDB id: 1v7z

Contents

Protein chains

(+ 0 more) 257 a.a. *

Ligands

SO4 ×18

CRN ×6

Metals

_MN ×6

_ZN ×6

Waters ×1835

* Residue conservation analysis

PDB id:

1v7z

Name:

Hydrolase

Title:

Creatininase-product complex

Structure:

Creatinine amidohydrolase. Chain: a, b, c, d, e, f. Synonym: creatininase. Engineered: yes

Source:

Pseudomonas sp.. Organism_taxid: 306. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Hexamer (from PQS)

Resolution:

1.60Å R-factor: 0.183 R-free: 0.198

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:

26-Dec-03 Release date: 27-Jan-04

Protein chains

P83772  (CRNA_PSEPU) -  Creatinine amidohydrolase from Pseudomonas putida

Seq: 260 a.a.

Struc: 257 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.2.10 - creatininase.
• Reaction: creatinine + H2O = creatine

creatinine + H2O = creatine (Bound ligand (Het Group name = CRN) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

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.