3KWC

Oxidized, active structure of the beta-carboxysomal gamma-Carbonic Anhydrase, CcmM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of the oxidative activation of the carboxysomal {gamma}-carbonic anhydrase, CcmM.

Pena, K.L.Castel, S.E.de Araujo, C.Espie, G.S.Kimber, M.S.

(2010) Proc Natl Acad Sci U S A 107: 2455-2460

  • DOI: https://doi.org/10.1073/pnas.0910866107
  • Primary Citation of Related Structures:  
    3KWC, 3KWD, 3KWE

  • PubMed Abstract: 

    Cyanobacterial RuBisCO is sequestered in large, icosahedral, protein-bounded microcompartments called carboxysomes. Bicarbonate is pumped into the cytosol, diffuses into the carboxysome through small pores in its shell, and is then converted to CO(2) by carbonic anhydrase (CA) prior to fixation. Paradoxically, many beta-cyanobacteria, including Thermosynechococcus elongatus BP-1, lack the conventional carboxysomal beta-CA, ccaA. The N-terminal domain of the carboxysomal protein CcmM is homologous to gamma-CA from Methanosarcina thermophila (Cam) but recombinant CcmM derived from ccaA-containing cyanobacteria show no CA activity. We demonstrate here that either full length CcmM from T. elongatus, or a construct truncated after 209 residues (CcmM209), is active as a CA-the first catalytically active bacterial gamma-CA reported. The 2.0 A structure of CcmM209 reveals a trimeric, left-handed beta-helix structure that closely resembles Cam, except that residues 198-207 form a third alpha-helix stabilized by an essential Cys194-Cys200 disulfide bond. Deleting residues 194-209 (CcmM193) results in an inactive protein whose 1.1 A structure shows disordering of the N- and C-termini, and reorganization of the trimeric interface and active site. Under reducing conditions, CcmM209 is similarly partially disordered and inactive as a CA. CcmM protein in fresh E. coli cell extracts is inactive, implying that the cellular reducing machinery can reduce and inactivate CcmM, while diamide, a thiol oxidizing agent, activates the enzyme. Thus, like membrane-bound eukaryotic cellular compartments, the beta-carboxysome appears to be able to maintain an oxidizing interior by precluding the entry of thioredoxin and other endogenous reducing agents.


  • Organizational Affiliation

    Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbon dioxide concentrating mechanism protein
A, B, C, D, E
A, B, C, D, E, F
229Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ccmMtll0944
EC: 4.2.1.1
UniProt
Find proteins for Q8DKB5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DKB5 
Go to UniProtKB:  Q8DKB5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DKB5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
H [auth A]
K [auth B]
M [auth C]
O [auth D]
Q [auth E]
H [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
U [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
IPA
Query on IPA

Download Ideal Coordinates CCD File 
G [auth A]
J [auth A]
L [auth B]
N [auth C]
R [auth E]
G [auth A],
J [auth A],
L [auth B],
N [auth C],
R [auth E],
S [auth E],
T [auth E]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A],
P [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.9α = 90
b = 105.04β = 90
c = 196.13γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XPREPdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description