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PDBsum entry 1i1h

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Isomerase PDB id
1i1h
Jmol
Contents
Protein chain
209 a.a. *
Ligands
COJ
Waters ×117
* Residue conservation analysis
PDB id:
1i1h
Name: Isomerase
Title: Crystal structure analysis of precorrin-8x methylmutase comp hydrogenobyrinic acid
Structure: Precorrin-8x methylmutase. Chain: a. Synonym: cobh. Engineered: yes
Source: Pseudomonas denitrificans. Organism_taxid: 43306. Gene: cobh. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
2.60Å     R-factor:   0.227     R-free:   0.218
Authors: L.W.Shipman,D.Li,C.A.Roessner,A.I.Scott,J.C.Sacchettini
Key ref:
L.W.Shipman et al. (2001). Crystal structure of precorrin-8x methyl mutase. Structure, 9, 587-596. PubMed id: 11470433 DOI: 10.1016/S0969-2126(01)00618-9
Date:
01-Feb-01     Release date:   18-Jul-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P21638  (COBH_PSEDE) -  Precorrin-8X methylmutase
Seq:
Struc:
210 a.a.
209 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.4.99.61  - Precorrin-8X methylmutase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Precorrin-8X = hydrogenobyrinate
Precorrin-8X
=
hydrogenobyrinate
Bound ligand (Het Group name = COJ)
corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cobalamin biosynthetic process   1 term 
  Biochemical function     isomerase activity     2 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/S0969-2126(01)00618-9 Structure 9:587-596 (2001)
PubMed id: 11470433  
 
 
Crystal structure of precorrin-8x methyl mutase.
L.W.Shipman, D.Li, C.A.Roessner, A.I.Scott, J.C.Sacchettini.
 
  ABSTRACT  
 
BACKGROUND: The crystal structure of precorrin-8x methyl mutase (CobH), an enzyme of the aerobic pathway to vitamin B12, provides evidence that the mechanism for methyl migration can plausibly be regarded as an allowed [1,5]-sigmatropic shift of a methyl group from C-11 to C-12 at the C ring of precorrin-8x to afford hydrogenobyrinic acid. RESULTS: The dimeric structure of CobH creates a set of shared active sites that readily discriminate between different tautomers of precorrin-8x and select a discrete tautomer for sigmatropic rearrangement. The active site contains a strictly conserved histidine residue close to the site of methyl migration in ring C of the substrate. CONCLUSION: Analysis of the structure with bound product suggests that the [1,5]-sigmatropic shift proceeds by protonation of the ring C nitrogen, leading to subsequent methyl migration.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Molecular Surface of the Complex with Hydrogenobyrinic Acid(a) A stereo representation of the contour of the binding cavity colored by electrostatic potential, with the A ring of the corrin at left front. Blue and red surfaces represent regions of positive and negative electrostatic potential, respectively. The surface around Arg116 (which closes the front of the cavity as depicted) is omitted for clearer illustration of the shape of the cavity.(b) The molecular surface of the bound CobH complex, illustrating the breadth of the binding cavity aperture.All ribbon diagrams and molecular graphics were created using SPOCK [33], unless otherwise noted

 
  The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 587-596) copyright 2001.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
15609338 M.E.Cuff, D.J.Miller, S.Korolev, X.Xu, W.F.Anderson, A.Edwards, A.Joachimiak, and A.Savchenko (2005).
Crystal structure of a predicted precorrin-8x methylmutase from Thermoplasma acidophilum.
  Proteins, 58, 751-754.
PDB code: 1ou0
12429089 J.P.Keller, P.M.Smith, J.Benach, D.Christendat, G.T.deTitta, and J.F.Hunt (2002).
The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase is a methyltransferase.
  Structure, 10, 1475-1487.
PDB codes: 1f38 1kxz 1l3b 1l3c 1l3i
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