2XWP

ANAEROBIC COBALT CHELATASE (CbiK) FROM SALMONELLA TYPHIMURIUM IN COMPLEX WITH METALATED TETRAPYRROLE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Evolution in a Family of Chelatases Facilitated by the Introduction of Active Site Asymmetry and Protein Oligomerization.

Romao, C.V., Ladakis, D., Lobo, S.A., Carrondo, M.A., Brindley, A.A., Deery, E., Matias, P.M., Pickersgill, R.W., Saraiva, L.M., Warren, M.J.

(2011) Proc Natl Acad Sci U S A 108: 97

  • DOI: 10.1073/pnas.1014298108
  • Primary Citation of Related Structures:  
    2XVX, 2XVZ, 2XWP, 2XWQ, 2XWS

  • PubMed Abstract: 

    • The class II chelatases associated with heme, siroheme, and cobalamin biosynthesis are structurally related enzymes that insert a specific metal ion (Fe(2+) or Co(2+)) into the center of a modified tetrapyrrole (protoporphyrin or sirohydrochlorin). The structures of two related class II enzymes, CbiX(S) from Archaeoglobus fulgidus and CbiK from Salmonella enterica, that are responsible for the insertion of cobalt along the cobalamin biosynthesis pathway are presented in complex with their metallated product ...

    The class II chelatases associated with heme, siroheme, and cobalamin biosynthesis are structurally related enzymes that insert a specific metal ion (Fe(2+) or Co(2+)) into the center of a modified tetrapyrrole (protoporphyrin or sirohydrochlorin). The structures of two related class II enzymes, CbiX(S) from Archaeoglobus fulgidus and CbiK from Salmonella enterica, that are responsible for the insertion of cobalt along the cobalamin biosynthesis pathway are presented in complex with their metallated product. A further structure of a CbiK from Desulfovibrio vulgaris Hildenborough reveals how cobalt is bound at the active site. The crystal structures show that the binding of sirohydrochlorin is distinctly different to porphyrin binding in the protoporphyrin ferrochelatases and provide a molecular overview of the mechanism of chelation. The structures also give insights into the evolution of chelatase form and function. Finally, the structure of a periplasmic form of Desulfovibrio vulgaris Hildenborough CbiK reveals a novel tetrameric arrangement of its subunits that are stabilized by the presence of a heme b cofactor. Whereas retaining colbaltochelatase activity, this protein has acquired a central cavity with the potential to chaperone or transport metals across the periplasmic space, thereby evolving a new use for an ancient protein subunit.

    Organizational Affiliation: 

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157 Oeiras, Portugal. cmromao@itqb.unl.pt



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SIROHYDROCHLORIN COBALTOCHELATASEA264Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
EC: 4.99.1.3
UniProt
Find proteins for Q05592 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q05592 
Go to UniProtKB:  Q05592
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05592
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SIR
Query on SIR
Download Ideal Coordinates CCD File 
B [auth A]COBALT SIROHYDROCHLORIN
C42 H44 Co N4 O16
CSFBERUGHBPUDZ-RQIVIIFKSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.63α = 90
b = 110.63β = 90
c = 89.53γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Advisory, Derived calculations, Other