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PDBsum entry 1rqb

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protein metals links
Transferase PDB id
1rqb
Jmol
Contents
Protein chain
472 a.a. *
Metals
_CO
Waters ×372
* Residue conservation analysis
PDB id:
1rqb
Name: Transferase
Title: Propionibacterium shermanii transcarboxylase 5s subunit
Structure: Transcarboxylase 5s subunit. Chain: a. Engineered: yes
Source: Propionibacterium freudenreichii subsp shermanii. Organism_taxid: 1752. Strain: subsp. Shermanii. Gene: 5s. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
1.90Å     R-factor:   0.162     R-free:   0.191
Authors: P.R.Hall,R.Zheng,L.Antony,M.Pusztai-Carey,P.R.Carey,V.C.Yee
Key ref:
P.R.Hall et al. (2004). Transcarboxylase 5S structures: assembly and catalytic mechanism of a multienzyme complex subunit. EMBO J, 23, 3621-3631. PubMed id: 15329673 DOI: 10.1038/sj.emboj.7600373
Date:
04-Dec-03     Release date:   07-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q70AC7  (5S_PROFR) -  Methylmalonyl-CoA carboxyltransferase 5S subunit
Seq:
Struc:
505 a.a.
472 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.1.3.1  - Methylmalonyl-CoA carboxytransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (S)-methylmalonyl-CoA + pyruvate = propanoyl-CoA + oxaloacetate
(S)-methylmalonyl-CoA
+ pyruvate
= propanoyl-CoA
+ oxaloacetate
      Cofactor: Biotin; Cobalt cation; Zn(2+)
Biotin
Cobalt cation
Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     catalytic activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1038/sj.emboj.7600373 EMBO J 23:3621-3631 (2004)
PubMed id: 15329673  
 
 
Transcarboxylase 5S structures: assembly and catalytic mechanism of a multienzyme complex subunit.
P.R.Hall, R.Zheng, L.Antony, M.Pusztai-Carey, P.R.Carey, V.C.Yee.
 
  ABSTRACT  
 
Transcarboxylase is a 1.2 million Dalton (Da) multienzyme complex from Propionibacterium shermanii that couples two carboxylation reactions, transferring CO(2)(-) from methylmalonyl-CoA to pyruvate to yield propionyl-CoA and oxaloacetate. Crystal structures of the 5S metalloenzyme subunit, which catalyzes the second carboxylation reaction, have been solved in free form and bound to its substrate pyruvate, product oxaloacetate, or inhibitor 2-ketobutyrate. The structure reveals a dimer of beta(8)alpha(8) barrels with an active site cobalt ion coordinated by a carbamylated lysine, except in the oxaloacetate complex in which the product's carboxylate group serves as a ligand instead. 5S and human pyruvate carboxylase (PC), an enzyme crucial to gluconeogenesis, catalyze similar reactions. A 5S-based homology model of the PC carboxyltransferase domain indicates a conserved mechanism and explains the molecular basis of mutations in lactic acidemia. PC disease mutations reproduced in 5S result in a similar decrease in carboxyltransferase activity and crystal structures with altered active sites.
 
  Selected figure(s)  
 
Figure 5.
Figure 5 Active sites of 5S complexes. The free 5S active site is shown with its Lys[C]184 (ball-and-stick with gray carbon atoms and bonds), cobalt ion (pink sphere), water ligands (red spheres), and side chains of residues which interact with either the cobalt ion or bound ligand. Superimposed are oxaloacetate (yellow), pyruvate (pale pink), and 2-ketobutyrate (cyan) ligands from their respective complexes.
Figure 6.
Figure 6 Active sites of 5S mutants. (A) Composite 5S active site showing the 5S-A59T crystal structure. The Thr59 side chain (orange and red ball-and-stick) interacts with Gln26, which in the complex structures forms hydrogen bonds with the bound ligands. For reference, oxaloacetate (yellow, as bound in 5S-oxal) and residues with which it interacts (Arg22 and Gln26), Met186 (gray, conformation in free 5S; pale pink, conformation in 5S-oxal), cobalt ion (pink sphere), and carbamylated Lys[C]184 are also shown. The orientation of this figure is related to that of Figure 5 by 90 rotation about the vertical axis combined with 90 rotation about the horizontal axis. (B) Composite 5S active site showing the 5S-M186I crystal structure. The I186 side chain (cyan ball-and-stick structure) would be expected to make close contacts with substrate or product; oxaloacetate (yellow, as bound in 5S-oxal) and Ala59 are shown for reference.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 3621-3631) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20668525 H.Falentin, S.M.Deutsch, G.Jan, V.Loux, A.Thierry, S.Parayre, M.B.Maillard, J.Dherbécourt, F.J.Cousin, J.Jardin, P.Siguier, A.Couloux, V.Barbe, B.Vacherie, P.Wincker, J.F.Gibrat, C.Gaillardin, and S.Lortal (2010).
The complete genome of Propionibacterium freudenreichii CIRM-BIA1, a hardy actinobacterium with food and probiotic applications.
  PLoS One, 5, e11748.  
20230056 S.Duangpan, S.Jitrapakdee, A.Adina-Zada, L.Byrne, T.N.Zeczycki, M.St Maurice, W.W.Cleland, J.C.Wallace, and P.V.Attwood (2010).
Probing the catalytic roles of Arg548 and Gln552 in the carboxyl transferase domain of the Rhizobium etli pyruvate carboxylase by site-directed mutagenesis.
  Biochemistry, 49, 3296-3304.  
20543879 T.Granjon, O.Maniti, Y.Auchli, P.Dahinden, R.Buchet, O.Marcillat, and P.Dimroth (2010).
Structure-function relations in oxaloacetate decarboxylase complex. Fluorescence and infrared approaches to monitor oxomalonate and Na(+) binding effect.
  PLoS One, 5, e10935.  
19213731 C.Y.Chou, L.P.Yu, and L.Tong (2009).
Crystal structure of biotin carboxylase in complex with substrates and implications for its catalytic mechanism.
  J Biol Chem, 284, 11690-11697.
PDB codes: 3g8c 3g8d
19523900 L.P.Yu, S.Xiang, G.Lasso, D.Gil, M.Valle, and L.Tong (2009).
A symmetrical tetramer for S. aureus pyruvate carboxylase in complex with coenzyme A.
  Structure, 17, 823-832.
PDB codes: 3hb9 3hbl 3ho8
19008230 P.D.Townsend, P.M.Holliday, S.Fenyk, K.C.Hess, M.A.Gray, D.R.Hodgson, and M.J.Cann (2009).
Stimulation of Mammalian G-protein-responsive Adenylyl Cyclases by Carbon Dioxide.
  J Biol Chem, 284, 784-791.  
19341298 T.N.Zeczycki, M.St Maurice, S.Jitrapakdee, J.C.Wallace, P.V.Attwood, and W.W.Cleland (2009).
Insight into the carboxyl transferase domain mechanism of pyruvate carboxylase from Rhizobium etli.
  Biochemistry, 48, 4305-4313.  
18613815 S.Jitrapakdee, M.St Maurice, I.Rayment, W.W.Cleland, J.C.Wallace, and P.V.Attwood (2008).
Structure, mechanism and regulation of pyruvate carboxylase.
  Biochem J, 413, 369-387.  
18297087 S.Xiang, and L.Tong (2008).
Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction.
  Nat Struct Mol Biol, 15, 295-302.
PDB codes: 3bg3 3bg5 3bg9
17400742 F.Li, C.H.Hagemeier, H.Seedorf, G.Gottschalk, and R.K.Thauer (2007).
Re-citrate synthase from Clostridium kluyveri is phylogenetically related to homocitrate synthase and isopropylmalate synthase rather than to Si-citrate synthase.
  J Bacteriol, 189, 4299-4304.  
17506874 J.D.Burman, C.E.Stevenson, R.G.Sawers, and D.M.Lawson (2007).
The crystal structure of Escherichia coli TdcF, a member of the highly conserved YjgF/YER057c/UK114 family.
  BMC Struct Biol, 7, 30.
PDB codes: 2uyj 2uyk 2uyn 2uyp
17717183 M.St Maurice, L.Reinhardt, K.H.Surinya, P.V.Attwood, J.C.Wallace, W.W.Cleland, and I.Rayment (2007).
Domain architecture of pyruvate carboxylase, a biotin-dependent multifunctional enzyme.
  Science, 317, 1076-1079.
PDB code: 2qf7
17316367 P.Z.Ozimek, S.H.Klompmaker, N.Visser, M.Veenhuis, and I.J.van der Klei (2007).
The transcarboxylase domain of pyruvate carboxylase is essential for assembly of the peroxisomal flavoenzyme alcohol oxidase.
  FEMS Yeast Res, 7, 1082-1092.  
17259315 S.Friedmann, B.E.Alber, and G.Fuchs (2007).
Properties of R-citramalyl-coenzyme A lyase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus.
  J Bacteriol, 189, 2906-2914.  
16330546 F.Forouhar, M.Hussain, R.Farid, J.Benach, M.Abashidze, W.C.Edstrom, S.M.Vorobiev, R.Xiao, T.B.Acton, Z.Fu, J.J.Kim, H.M.Miziorko, G.T.Montelione, and J.F.Hunt (2006).
Crystal structures of two bacterial 3-hydroxy-3-methylglutaryl-CoA lyases suggest a common catalytic mechanism among a family of TIM barrel metalloenzymes cleaving carbon-carbon bonds.
  J Biol Chem, 281, 7533-7545.
PDB codes: 1ydn 1ydo
16599820 P.R.Carey (2006).
Raman crystallography and other biochemical applications of Raman microscopy.
  Annu Rev Phys Chem, 57, 527-554.  
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.