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PDBsum entry 1qgo
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Metal binding protein PDB id
1qgo

 

 

 

 

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Contents
Protein chain
257 a.a. *
Ligands
SO4 ×3
Waters ×226
* Residue conservation analysis
PDB id:
1qgo
Name: Metal binding protein
Title: Anaerobic cobalt chelatase in cobalamin biosynthesis from salmonella typhimurium
Structure: Anaerobic cobalamin biosynthetic cobalt chelatase. Chain: a. Synonym: cbik protein. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 99287. Strain: lt2. Gene: cbik. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: lyss. Other_details: his-tagged recombinant gene
Biol. unit: Monomer (from PDB file)
Resolution:
2.40Å     R-factor:   0.208     R-free:   0.271
Authors: H.L.Schubert,E.Raux,M.J.Warren,K.S.Wilson
Key ref:
H.L.Schubert et al. (1999). Common chelatase design in the branched tetrapyrrole pathways of heme and anaerobic cobalamin synthesis. Biochemistry, 38, 10660-10669. PubMed id: 10451360 DOI: 10.1021/bi9906773
Date:
03-May-99     Release date:   29-Sep-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q05592  (CBIK_SALTY) -  Sirohydrochlorin cobaltochelatase from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Seq:
Struc: 		264 a.a.
257 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.99.1.3  - sirohydrochlorin cobaltochelatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Corrin and Siroheme Biosynthesis (part 2)
      Reaction:
1. Co-sirohydrochlorin + 2 H+ = sirohydrochlorin + Co2+
2. Co-precorrin-2 + 3 H+ = precorrin-2 + Co2+
Co-sirohydrochlorin
 + 2 × H(+)
 = sirohydrochlorin
 + Co(2+)
Co-precorrin-2
 + 3 × H(+)
 = precorrin-2
 + Co(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1021/bi9906773 Biochemistry 38:10660-10669 (1999)
PubMed id: 10451360  
 
 
Common chelatase design in the branched tetrapyrrole pathways of heme and anaerobic cobalamin synthesis.
H.L.Schubert, E.Raux, K.S.Wilson, M.J.Warren.
 
  ABSTRACT  
 
Prosthetic groups such as heme, chlorophyll, and cobalamin (vitamin B(12)) are characterized by their branched biosynthetic pathway and unique metal insertion steps. The metal ion chelatases can be broadly classed either as single-subunit ATP-independent enzymes, such as the anaerobic cobalt chelatase and the protoporphyrin IX (PPIX) ferrochelatase, or as heterotrimeric, ATP-dependent enzymes, such as the Mg chelatase involved in chlorophyll biosynthesis. The X-ray structure of the anaerobic cobalt chelatase from Salmonella typhimurium, CbiK, has been solved to 2.4 A resolution. Despite a lack of significant amino acid sequence similarity, the protein structure is homologous to that of Bacillus subtilis PPIX ferrochelatase. Both enzymes contain a histidine residue previously identified as the metal ion ligand, but CbiK contains a second histidine in place of the glutamic acid residue identified as a general base in PPIX ferrochelatase. Site-directed mutagenesis has confirmed a role for this histidine and a nearby glutamic acid in cobalt binding, modulating metal ion specificity as well as catalytic efficiency. Contrary to the predicted protoporphyrin binding site in PPIX ferrochelatase, the precorrin-2 binding site in CbiK is clearly defined within a large horizontal cleft between the N- and C-terminal domains. The structural similarity has implications for the understanding of the evolution of this branched biosynthetic pathway.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21173279 C.V.Romão, D.Ladakis, S.A.Lobo, M.A.Carrondo, A.A.Brindley, E.Deery, P.M.Matias, R.W.Pickersgill, L.M.Saraiva, and M.J.Warren (2011).
Evolution in a family of chelatases facilitated by the introduction of active site asymmetry and protein oligomerization.
  Proc Natl Acad Sci U S A, 108, 97.
PDB codes: 2xvx 2xvz 2xwp 2xwq 2xws
  20592802 B.C.Tripathy, I.Sherameti, and R.Oelmüller (2010).
Siroheme: an essential component for life on earth.
  Plant Signal Behav, 5, 14-20.  
20223218 J.Lundqvist, H.Elmlund, R.P.Wulff, L.Berglund, D.Elmlund, C.Emanuelsson, H.Hebert, R.D.Willows, M.Hansson, M.Lindahl, and S.Al-Karadaghi (2010).
ATP-induced conformational dynamics in the AAA+ motor unit of magnesium chelatase.
  Structure, 18, 354-365.
PDB code: 2x31
18593702 G.A.Hunter, M.P.Sampson, and G.C.Ferreira (2008).
Metal ion substrate inhibition of ferrochelatase.
  J Biol Chem, 283, 23685-23691.  
18588505 H.L.Schubert, R.S.Rose, H.K.Leech, A.A.Brindley, C.P.Hill, S.E.Rigby, and M.J.Warren (2008).
Structure and function of SirC from Bacillus megaterium: a metal-binding precorrin-2 dehydrogenase.
  Biochem J, 415, 257-263.
PDB code: 3dfz
18423489 T.Karlberg, M.D.Hansson, R.K.Yengo, R.Johansson, H.O.Thorvaldsen, G.C.Ferreira, M.Hansson, and S.Al-Karadaghi (2008).
Porphyrin binding and distortion and substrate specificity in the ferrochelatase reaction: the role of active site residues.
  J Mol Biol, 378, 1074-1083.
PDB codes: 2q2n 2q2o 2q3j
17898893 G.L.Holliday, J.M.Thornton, A.Marquet, A.G.Smith, F.Rébeillé, R.Mendel, H.L.Schubert, A.D.Lawrence, and M.J.Warren (2007).
Evolution of enzymes and pathways for the biosynthesis of cofactors.
  Nat Prod Rep, 24, 972-987.  
17898892 R.R.Mendel, A.G.Smith, A.Marquet, and M.J.Warren (2007).
Metal and cofactor insertion.
  Nat Prod Rep, 24, 963-971.  
16650981 A.Andreeva, and A.G.Murzin (2006).
Evolution of protein fold in the presence of functional constraints.
  Curr Opin Struct Biol, 16, 399-408.  
16835730 J.Yin, L.X.Xu, M.M.Cherney, E.Raux-Deery, A.A.Bindley, A.Savchenko, J.R.Walker, M.E.Cuff, M.J.Warren, and M.N.James (2006).
Crystal structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus.
  J Struct Funct Genomics, 7, 37-50.
PDB code: 2dj5
16453119 M.D.Hansson, M.Lindstam, and M.Hansson (2006).
Crosstalk between metal ions in Bacillus subtilis ferrochelatase.
  J Biol Inorg Chem, 11, 325-333.  
15545265 E.Raux-Deery, H.K.Leech, K.A.Nakrieko, K.J.McLean, A.W.Munro, P.Heathcote, S.E.Rigby, A.G.Smith, and M.J.Warren (2005).
Identification and characterization of the terminal enzyme of siroheme biosynthesis from Arabidopsis thaliana: a plastid-located sirohydrochlorin ferrochelatase containing a 2FE-2S center.
  J Biol Chem, 280, 4713-4721.  
12686546 A.A.Brindley, E.Raux, H.K.Leech, H.L.Schubert, and M.J.Warren (2003).
A story of chelatase evolution: identification and characterization of a small 13-15-kDa "ancestral" cobaltochelatase (CbiXS) in the archaea.
  J Biol Chem, 278, 22388-22395.  
12869542 D.A.Rodionov, A.G.Vitreschak, A.A.Mironov, and M.S.Gelfand (2003).
Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes.
  J Biol Chem, 278, 41148-41159.  
12917443 H.K.Leech, E.Raux, K.J.McLean, A.W.Munro, N.J.Robinson, G.P.Borrelly, M.Malten, D.Jahn, S.E.Rigby, P.Heathcote, and M.J.Warren (2003).
Characterization of the cobaltochelatase CbiXL: evidence for a 4Fe-4S center housed within an MXCXXC motif.
  J Biol Chem, 278, 41900-41907.  
12758040 J.E.Cornah, M.J.Terry, and A.G.Smith (2003).
Green or red: what stops the traffic in the tetrapyrrole pathway?
  Trends Plant Sci, 8, 224-230.  
14595395 M.E.Stroupe, H.K.Leech, D.S.Daniels, M.J.Warren, and E.D.Getzoff (2003).
CysG structure reveals tetrapyrrole-binding features and novel regulation of siroheme biosynthesis.
  Nat Struct Biol, 10, 1064-1073.
PDB codes: 1pjq 1pjs 1pjt
12388743 C.A.Whittaker, and R.O.Hynes (2002).
Distribution and evolution of von Willebrand/integrin A domains: widely dispersed domains with roles in cell adhesion and elsewhere.
  Mol Biol Cell, 13, 3369-3387.  
11980703 H.L.Schubert, E.Raux, A.A.Brindley, H.K.Leech, K.S.Wilson, C.P.Hill, and M.J.Warren (2002).
The structure of Saccharomyces cerevisiae Met8p, a bifunctional dehydrogenase and ferrochelatase.
  EMBO J, 21, 2068-2075.
PDB code: 1kyq
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
11053391 S.G.Dashper, A.Hendtlass, N.Slakeski, C.Jackson, K.J.Cross, L.Brownfield, R.Hamilton, I.Barr, and E.C.Reynolds (2000).
Characterization of a novel outer membrane hemin-binding protein of Porphyromonas gingivalis.
  J Bacteriol, 182, 6456-6462.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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