1QRL

A CLOSER LOOK AT THE ACTIVE SITE OF GAMMA-CARBONIC ANHYDRASES: HIGH RESOLUTION CRYSTALLOGRAPHIC STUDIES OF THE CARBONIC ANHYDRASE FROM METHANOSARCINA THERMOPHILA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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

(2000) Biochemistry 39: 9222-9231

  • Primary Citation of Related Structures:  1QQ0, 1QRE, 1QRF, 1QRG, 1QRM

  • PubMed 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 ...

    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.


    Related Citations: 
    • A Left-Handed Beta-Helix Revealed by the Crystal Structure of the Carbonic Anhydrase from Methanosarcina thermophila
      Kisker, C.,Schindelin, H.,Alber, B.,Ferry, J.,Rees, D.
      (1996) Embo J. 15: 2323


    Organizational Affiliation

    Graduate Option in Biochemistry, California Institute of Technology, Pasadena 91125, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CARBONIC ANHYDRASE
A
214Methanosarcina thermophilaEC: 4.2.1.1
Find proteins for P40881 (Methanosarcina thermophila)
Go to UniProtKB:  P40881
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

Download SDF File 
Download CCD File 
A
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BCTKi: 6700000 - 42000000 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.183 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 82.513α = 90.00
b = 82.513β = 90.00
c = 82.513γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-25
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance