4UN1

Sirohaem decarboxylase AhbA/B - an enzyme with structural homology to the Lrp/AsnC transcription factor family that is part of the alternative haem biosynthesis pathway.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Structure, Function and Properties of Sirohaem Decarboxylase - an Enzyme with Structural Homology to a Transcription Factor Family that is Part of the Alternative Haem Biosynthesis Pathway.

Palmer, D.J.Schroeder, S.Lawrence, A.D.Deery, E.Lobo, S.A.Saraiva, L.M.Mclean, K.J.Munro, A.W.Ferguson, S.J.Pickersgill, R.W.Brown, D.G.Warren, M.J.

(2014) Mol.Microbiol. 93: 247

  • DOI: 10.1111/mmi.12656
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Some bacteria and archaea synthesize haem by an alternative pathway, which involves the sequestration of sirohaem as a metabolic intermediate rather than as a prosthetic group. Along this pathway the two acetic acid side-chains attached to C12 and C1 ...

    Some bacteria and archaea synthesize haem by an alternative pathway, which involves the sequestration of sirohaem as a metabolic intermediate rather than as a prosthetic group. Along this pathway the two acetic acid side-chains attached to C12 and C18 are decarboxylated by sirohaem decarboxylase, a heterodimeric enzyme composed of AhbA and AhbB, to give didecarboxysirohaem. Further modifications catalysed by two related radical SAM enzymes, AhbC and AhbD, transform didecarboxysirohaem into Fe-coproporphyrin III and haem respectively. The characterization of sirohaem decarboxylase is reported in molecular detail. Recombinant versions of Desulfovibrio desulfuricans, Desulfovibrio vulgaris and Methanosarcina barkeri AhbA/B have been produced and their physical properties compared. The D. vulgaris and M. barkeri enzyme complexes both copurify with haem, whose redox state influences the activity of the latter. The kinetic parameters of the D. desulfuricans enzyme have been determined, the enzyme crystallized and its structure has been elucidated. The topology of the enzyme reveals that it shares a structural similarity to the AsnC/Lrp family of transcription factors. The active site is formed in the cavity between the two subunits and a AhbA/B-product complex with didecarboxysirohaem has been obtained. A mechanism for the decarboxylation of the kinetically stable carboxyl groups is proposed.


    Organizational Affiliation

    School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent, CT2 7NJ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY
A, C
173Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949)Mutation(s): 0 
Find proteins for B8J364 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949))
Go to UniProtKB:  B8J364
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY
B, D
179Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949)Mutation(s): 0 
Find proteins for B8J3A4 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949))
Go to UniProtKB:  B8J3A4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OBV
Query on OBV

Download SDF File 
Download CCD File 
B, C
12,18-DIDECARBOXY-SIROHEME
C40 H44 Fe N4 O12
IWKGTOOPBQHBLV-XOLYYWOLSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.300α = 90.00
b = 78.600β = 90.00
c = 150.300γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2014-07-30
    Type: Database references