PDBsum entry 1aln

Hydrolase

PDB id: 1aln

Contents

Protein chain

294 a.a. *

Ligands

CTD

Metals

_ZN

Waters ×49

* Residue conservation analysis

PDB id:

1aln

Name:

Hydrolase

Title:

Crystal structure of cytidine deaminase complexed with 3-deazacytidine

Structure:

Cytidine deaminase. Chain: a. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Homo-Dimer (from PDB file)

Resolution:

2.30Å R-factor: 0.190

Authors:

S.Xiang,C.W.Carter

Key ref:

S.Xiang et al. (1996). Cytidine deaminase complexed to 3-deazacytidine: a "valence buffer" in zinc enzyme catalysis. Biochemistry, 35, 1335-1341. PubMed id: 8634261 DOI: 10.1021/bi9525583

Date:

02-Jun-97 Release date: 17-Sep-97

Protein chain

P0ABF6  (CDD_ECOLI) -  Cytidine deaminase from Escherichia coli (strain K12)

Seq: 294 a.a.

Struc: 294 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.4.5 - cytidine deaminase.
• Reaction:
  1. cytidine + H2O + H⁺ = uridine + NH4⁺
  2. 2'-deoxycytidine + H2O + H⁺ = 2'-deoxyuridine + NH4⁺

cytidine (Bound ligand (Het Group name = CTD) matches with 88.89% similarity) + H2O + H(+) = uridine + NH4(+)

2'-deoxycytidine (Bound ligand (Het Group name = CTD) matches with 83.33% similarity) + H2O + H(+) = 2'-deoxyuridine + NH4(+)

• Cofactor: Zn(2+)

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

reference

DOI no: 10.1021/bi9525583

Biochemistry 35:1335-1341 (1996)

PubMed id: 8634261

Cytidine deaminase complexed to 3-deazacytidine: a "valence buffer" in zinc enzyme catalysis.

S.Xiang, S.A.Short, R.Wolfenden, C.W.Carter.

ABSTRACT

The cytidine deaminase substrate analog inhibitor 3-deazacytidine binds with its 4-amino group inserted into a site previously identified as a probable binding site for the leaving ammonia group. Binding to this site shifts the pyrimidine ring significantly further from the activated water molecule than the position it occupies in either of two complexes with compounds capable of hydrogen bonding at the 3-position of the ring [Xiang et al. (1995) Biochemistry 34, 4516-4523]. Difference Fourier maps between the deazacytidine, dihydrozebularine, and zebularine--hydrate inhibitor complexes suggest that the ring itself moves successively toward the activated water, leaving the amino group behind in this site as the substrate complex approaches the transition state. They also reveal systematic changes in a single zinc-sulfur bond distance. These correlate with chemical changes expected as the substrate approaches the tetrahedral transition state, in which the zinc-activated hydroxyl group develops maximal negative charge and forms a short hydrogen bond to the neighboring carboxylate group of Glu 104. Empirical bond valence relationships suggest that the Zn-S gamma 132 bond functions throughout the reaction as a "valence buffer" that accommodates changing negative charge on the hydroxyl group. Similar structural features in alcohol dehydrogenase suggest that analogous mechanisms may be a general feature of catalysis by zinc enzymes.