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 
  • R-Value Observed: 0.205 

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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:  
    4CZD, 4UN1

  • 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 C18 are decarboxylated by sirohaem decarboxylase, a heterodimeric enzyme composed of AhbA and AhbB, to give didecarboxysirohaem ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILYA, C173Desulfovibrio desulfuricansMutation(s): 0 
EC: 4.1.1.111
UniProt
Find proteins for B8J364 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB))
Explore B8J364 
Go to UniProtKB:  B8J364
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILYB, D179Desulfovibrio desulfuricansMutation(s): 0 
EC: 4.1.1.111
UniProt
Find proteins for B8J3A4 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB))
Explore B8J3A4 
Go to UniProtKB:  B8J3A4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OBV (Subject of Investigation/LOI)
Query on OBV

Download Ideal Coordinates CCD File 
E [auth B], F [auth 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 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.3α = 90
b = 78.6β = 90
c = 150.3γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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