PDBsum entry 1bv3

Lyase

PDB id: 1bv3

Contents

Protein chain

257 a.a. *

Ligands

HGB

URE

Metals

_ZN

Waters ×134

* Residue conservation analysis

PDB id:

1bv3

Name:

Lyase

Title:

Human carbonic anhydrase ii complexed with urea

Structure:

Protein (carbonic anhydrase ii). Chain: a. Synonym: hca ii. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Cell: erythrocytes. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.85Å R-factor: 0.171 R-free: 0.213

Authors:

F.Briganti,S.Mangani,A.Scozzafava,G.Vernaglione,C.T.Supuran

Key ref:

F.Briganti et al. (1999). Carbonic anhydrase catalyzes cyanamide hydration to urea: is it mimicking the physiological reaction? J Biol Inorg Chem, 4, 528-536. PubMed id: 10550681

Date:

22-Sep-98 Release date: 28-Sep-99

Protein chain

P00918  (CAH2_HUMAN) -  Carbonic anhydrase 2 from Homo sapiens

Seq: 260 a.a.

Struc: 257 a.a.

Enzyme reactions

• Enzyme class 2: E.C.4.2.1.1 - carbonic anhydrase.
• Reaction: hydrogencarbonate + H⁺ = CO2 + H2O

hydrogencarbonate + H(+) = CO2 (Bound ligand (Het Group name = URE) matches with 40.00% similarity) + H2O

• Cofactor: Zn(2+)
• Enzyme class 3: E.C.4.2.1.69 - cyanamide hydratase.
• Reaction: urea = cyanamide + H2O

urea (Bound ligand (Het Group name = URE) corresponds exactly) = cyanamide + H2O

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

J Biol Inorg Chem 4:528-536 (1999)

PubMed id: 10550681

Carbonic anhydrase catalyzes cyanamide hydration to urea: is it mimicking the physiological reaction?

F.Briganti, S.Mangani, A.Scozzafava, G.Vernaglione, C.T.Supuran.

ABSTRACT

The interaction of human carbonic anhydrase (hCA) isozymes I and II with cyanamide, a linear molecule isoelectronic with the main physiological substrate of the enzyme, CO(2), was investigated through spectroscopic, kinetic, and X-ray crystallographic studies. We show here that cyanamide is hydrated to urea in the presence of CAs, and that it also acts as a weak non-competitive inhibitor (K(I)=61+/-3 mM and 238+/-9 mM for hCA II and hCA I, respectively) towards the esterasic activity of these enzymes, as tested with 4-nitrophenyl acetate. Changes in the spectrum of the Co(II)-hCA II derivative observed in the presence of cyanamide suggest that it likely binds the metal ion within the CA active site, adding to the coordination sphere, not substituting the metal-bound solvent molecule. It thereafter undergoes a nucleophilic attack from the metal-bound hydroxide ion, forming urea which remains bound to the metal, as observed in the X-ray crystal structure of hCA II soaked in cyanamide solutions for several hours. The urea molecule is directly coordinated to the active site Zn(II) ion through a protonated nitrogen atom. Several hydrogen bonds involving active site residues Thr199 and Thr200 as well as three water molecules (Wat99, Wat122, and Wat123) further stabilize the urea-hCA II adduct. Kinetic studies in solution further proved that urea acts as a tight binding inhibitor of the two isozymes hCA I and hCA II, with very slow binding kinetics (k(on) = 2.5 x 10(-5)s(-1)M(-1)). A mechanism to explain the hydration process of cyanamide by CAs, as well as the tight binding of urea in the active site, is also proposed based on the hypothesis that urea is deprotonated when bound to the enzyme. Cyanamide is thus the first true suicide substrate of this enzyme for which binding has been documented by means of X-ray crystallographic and spectroscopic studies.