3TIS

Crystal structures of yrdA from Escherichia coli, a homologous protein of gamma-class carbonic anhydrases, show possible allosteric conformations


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

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Literature

Structures of the gamma-class carbonic anhydrase homologue YrdA suggest a possible allosteric switch

Park, H.M.Park, J.H.Choi, J.W.Lee, J.E.Kim, B.Y.Jung, C.H.Kim, J.S.

(2012) Acta Crystallogr D Biol Crystallogr 68: 920-926

  • DOI: 10.1107/S0907444912017210
  • Primary Citation of Related Structures:  
    3TIO, 3TIS

  • PubMed Abstract: 
  • The YrdA protein shows high sequence similarity to γ-class carbonic anhydrase (γ-CA) proteins and is classified as part of the γ-CA protein family. However, its function has not been fully elucidated as it lacks several of the conserved residues that are considered to be necessary for γ-CA catalysis ...

    The YrdA protein shows high sequence similarity to γ-class carbonic anhydrase (γ-CA) proteins and is classified as part of the γ-CA protein family. However, its function has not been fully elucidated as it lacks several of the conserved residues that are considered to be necessary for γ-CA catalysis. Interestingly, a homologue of γ-CA from Methanosarcina thermophila and a β-carboxysomal γ-CA from a β-cyanobacterium have shown that these catalytic residues are not always conserved in γ-CAs. The crystal structure of YrdA from Escherichia coli (ecYrdA) is reported here in two crystallographic forms. The overall structure of ecYrdA is also similar to those of the γ-CAs. One loop around the putative catalytic site shows a number of alternative conformations. A His residue (His70) on this loop coordinates with, or is reoriented from, the catalytic Zn(2+) ion; this is similar to the conformations mediated by an Asp residue on the catalytic loops of β-CA proteins. One Trp residue (Trp171) also adopts two alternative conformations that may be related to the spatial positions of the catalytic loop. Even though significant CA activity could not be detected using purified ecYrdA, these structural features have potential functional implications for γ-CA-related proteins.


    Organizational Affiliation

    Department of Chemistry and Institute of Basic Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, Republic of Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein YrdAA, B, C183Escherichia coli K-12Mutation(s): 1 
Gene Names: yrdAb3279JW5710
UniProt
Find proteins for P0A9W9 (Escherichia coli (strain K12))
Explore P0A9W9 
Go to UniProtKB:  P0A9W9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A], E [auth B], F [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.793α = 90
b = 96.793β = 90
c = 87.398γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-01
    Type: Initial release
  • Version 1.1: 2012-08-29
    Changes: Database references