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PDBsum entry 1xvt

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Transferase PDB id
1xvt
Jmol PyMol
Contents
Protein chain
402 a.a. *
Ligands
COA
Waters ×80
* Residue conservation analysis
PDB id:
1xvt
Name: Transferase
Title: Crystal structure of native caib in complex with coenzyme a
Structure: Crotonobetainyl-coa:carnitine coa-transferase. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: caib. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.199     R-free:   0.237
Authors: E.S.Rangarajan,Y.Li,P.Iannuzzi,M.Cygler,A.Matte
Key ref:
E.S.Rangarajan et al. (2005). Crystal structure of Escherichia coli crotonobetainyl-CoA: carnitine CoA-transferase (CaiB) and its complexes with CoA and carnitinyl-CoA. Biochemistry, 44, 5728-5738. PubMed id: 15823031 DOI: 10.1021/bi047656f
Date:
28-Oct-04     Release date:   15-Mar-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P31572  (CAIB_ECOLI) -  L-carnitine CoA-transferase
Seq:
Struc:
405 a.a.
402 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.8.3.21  - L-carnitine CoA-transferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. (E)-4-(trimethylammonio)but-2-enoyl-CoA + L-carnitine = (E)-4- (trimethylammonio)but-2-enoate + L-carnitinyl-CoA
2. 4-trimethylammoniobutanoyl-CoA + L-carnitine = 4-trimethylammoniobutanoate + L-carnitinyl-CoA
(E)-4-(trimethylammonio)but-2-enoyl-CoA
+ L-carnitine
= (E)-4- (trimethylammonio)but-2-enoate
+ L-carnitinyl-CoA
4-trimethylammoniobutanoyl-CoA
+ L-carnitine
= 4-trimethylammoniobutanoate
+ L-carnitinyl-CoA
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     carnitine metabolic process   2 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi047656f Biochemistry 44:5728-5738 (2005)
PubMed id: 15823031  
 
 
Crystal structure of Escherichia coli crotonobetainyl-CoA: carnitine CoA-transferase (CaiB) and its complexes with CoA and carnitinyl-CoA.
E.S.Rangarajan, Y.Li, P.Iannuzzi, M.Cygler, A.Matte.
 
  ABSTRACT  
 
L-Carnitine (R-[-]-3-hydroxy-4-trimethylaminobutyrate) is found in both eukaryotic and prokaryotic cells and participates in diverse processes including long-chain fatty-acid transport and osmoprotection. The enzyme crotonobetainyl/gamma-butyrobetainyl-CoA:carnitine CoA-transferase (CaiB; E.C. 2.8.3.-) catalyzes the first step in carnitine metabolism, leading to the final product gamma-butyrobetaine. The crystal structures of Escherichia coli apo-CaiB, as well as its Asp169Ala mutant bound to CoA and to carnitinyl-CoA, have been determined and refined to 1.6, 2.4, and 2.4 A resolution, respectively. CaiB is composed of two identical circular chains that together form an intertwined dimer. Each monomer consists of a large domain, containing a Rossmann fold, and a small domain. The monomer and dimer resemble those of formyl-CoA transferase from Oxalobacter formigenes, as well as E. coli YfdW, a putative type-III CoA transferase of unknown function. The CoA cofactor-binding site is formed at the interface of the large domain of one monomer and the small domain from the second monomer. Most of the protein-CoA interactions are formed with the Rossmann fold domain. While the location of cofactor binding is similar in the three proteins, the specific CoA-protein interactions vary somewhat between CaiB, formyl-CoA transferase, and YfdW. CoA binding results in a change in the relative positions of the large and small domains compared with apo-CaiB. The observed carnitinyl-CoA product in crystals of the CaiB Asp169Ala mutant cocrystallized with crotonoyl-CoA and carnitine could result from (i) a catalytic mechanism involving a ternary enzyme-substrate complex, independent of a covalent anhydride intermediate with Asp169, (ii) a spontaneous reaction of the substrates in solution, followed by binding to the enzyme, or (iii) an involvement of another residue substituting functionally for Asp169, such as Glu23.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19955419 J.Zarzycki, V.Brecht, M.Müller, and G.Fuchs (2009).
Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus.
  Proc Natl Acad Sci U S A, 106, 21317-21322.  
18162462 C.L.Berthold, C.G.Toyota, N.G.Richards, and Y.Lindqvist (2008).
Reinvestigation of the catalytic mechanism of formyl-CoA transferase, a class III CoA-transferase.
  J Biol Chem, 283, 6519-6529.
PDB codes: 2vjk 2vjl 2vjm 2vjn 2vjo
17272727 J.D.Todd, R.Rogers, Y.G.Li, M.Wexler, P.L.Bond, L.Sun, A.R.Curson, G.Malin, M.Steinke, and A.W.Johnston (2007).
Structural and regulatory genes required to make the gas dimethyl sulfide in bacteria.
  Science, 315, 666-669.  
16547052 S.Friedmann, A.Steindorf, B.E.Alber, and G.Fuchs (2006).
Properties of succinyl-coenzyme A:L-malate coenzyme A transferase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus.
  J Bacteriol, 188, 2646-2655.  
16952935 S.Friedmann, B.E.Alber, and G.Fuchs (2006).
Properties of succinyl-coenzyme A:D-citramalate coenzyme A transferase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus.
  J Bacteriol, 188, 6460-6468.  
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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