PDBsum entry 1qq0

Lyase

PDB id: 1qq0

Contents

Protein chain

208 a.a. *

Metals

_CO

Waters ×79

* Residue conservation analysis

PDB id:

1qq0

Name:

Lyase

Title:

Cobalt substituted carbonic anhydrase from methanosarcina thermophila

Structure:

Carbonic anhydrase. Chain: a. Engineered: yes

Source:

Methanosarcina thermophila. Organism_taxid: 2210. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Trimer (from PDB file)

Resolution:

1.76Å R-factor: 0.189 R-free: 0.217

Authors:

T.M.Iverson,B.E.Alber,C.Kisker,J.G.Ferry,D.C.Rees

Key ref:

T.M.Iverson et al. (2000). A closer look at the active site of gamma-class carbonic anhydrases: high-resolution crystallographic studies of the carbonic anhydrase from Methanosarcina thermophila. Biochemistry, 39, 9222-9231. PubMed id: 10924115 DOI: 10.1021/bi000204s

Date:

10-Jun-99 Release date: 24-Jun-99

Protein chain

P40881  (CAH_METTT) -  Carbonic anhydrase from Methanosarcina thermophila (strain ATCC 43570 / DSM 1825 / OCM 12 / VKM B-1830 / TM-1)

Seq: 247 a.a.

Struc: 208 a.a.

Enzyme reactions

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

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

Added reference

DOI no: 10.1021/bi000204s

Biochemistry 39:9222-9231 (2000)

PubMed id: 10924115

A closer look at the active site of gamma-class carbonic anhydrases: high-resolution crystallographic studies of the carbonic anhydrase from Methanosarcina thermophila.

T.M.Iverson, B.E.Alber, C.Kisker, J.G.Ferry, D.C.Rees.

ABSTRACT

The prototype of the gamma-class of carbonic anhydrase has been characterized from the methanogenic archaeon Methanosarcina thermophila. Previously reported kinetic studies of the gamma-class carbonic anhydrase are consistent with this enzyme having a reaction mechanism similar to that of the mammalian alpha-class carbonic anhydrase. However, the overall folds of these two enzymes are dissimilar, and apart from the zinc-coordinating histidines, the active site residues bear little resemblance to one another. The crystal structures of zinc-containing and cobalt-substituted gamma-class carbonic anhydrases from M. thermophila are reported here between 1.46 and 1.95 A resolution in the unbound form and cocrystallized with either SO(4)(2)(-) or HCO(3)(-). Relative to the tetrahedral coordination geometry seen at the active site in the alpha-class of carbonic anhydrases, the active site of the gamma-class enzyme contains additional metal-bound water ligands, so the overall coordination geometry is trigonal bipyramidal for the zinc-containing enzyme and octahedral for the cobalt-substituted enzyme. Ligands bound to the active site all make contacts with the side chain of Glu 62 in manners that suggest the side chain is likely protonated. In the uncomplexed zinc-containing enzyme, the side chains of Glu 62 and Glu 84 appear to share a proton; additionally, Glu 84 exhibits multiple conformations. This suggests that Glu 84 may act as a proton shuttle, which is an important aspect of the reaction mechanism of alpha-class carbonic anhydrases. A hydrophobic pocket on the surface of the enzyme may participate in the trapping of CO(2) at the active site. On the basis of the coordination geometry at the active site, ligand binding modes, the behavior of the side chains of Glu 62 and Glu 84, and analogies to the well-characterized alpha-class of carbonic anhydrases, a more-defined reaction mechanism is proposed for the gamma-class of carbonic anhydrases.