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PDBsum entry 1x74

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protein ligands Protein-protein interface(s) links
Isomerase PDB id
1x74
Jmol
Contents
Protein chains
354 a.a. *
Ligands
GOL ×15
PO4
Waters ×1458
* Residue conservation analysis
PDB id:
1x74
Name: Isomerase
Title: Alpha-methylacyl-coa racemase from mycobacterium tuberculosi mutational and structural characterization of the fold and site
Structure: 2-methylacyl-coa racemase. Chain: a, b, c, d. Synonym: alpha-methylacyl-coa racemase. Engineered: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 1773. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.79Å     R-factor:   0.162     R-free:   0.193
Authors: S.Kalle,P.Bhaumik,W.Schmitz,T.J.Kotti,E.Conzelmann,R.K.Wiere J.K.Hiltunen
Key ref:
K.Savolainen et al. (2005). Alpha-methylacyl-CoA racemase from Mycobacterium tuberculosis. Mutational and structural characterization of the active site and the fold. J Biol Chem, 280, 12611-12620. PubMed id: 15632186 DOI: 10.1074/jbc.M409704200
Date:
13-Aug-04     Release date:   18-Jan-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O06543  (O06543_MYCTU) -  Alpha-methylacyl-CoA racemase Mcr
Seq:
Struc:
360 a.a.
354 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
DOI no: 10.1074/jbc.M409704200 J Biol Chem 280:12611-12620 (2005)
PubMed id: 15632186  
 
 
Alpha-methylacyl-CoA racemase from Mycobacterium tuberculosis. Mutational and structural characterization of the active site and the fold.
K.Savolainen, P.Bhaumik, W.Schmitz, T.J.Kotti, E.Conzelmann, R.K.Wierenga, J.K.Hiltunen.
 
  ABSTRACT  
 
Alpha-methylacyl-CoA racemase (Amacr) catalyzes the racemization of alpha-methyl-branched CoA esters. Sequence comparisons have shown that this enzyme is a member of the family III CoA transferases. The mammalian Amacr is involved in bile acid synthesis and branched-chain fatty acid degradation. In human, mutated variants of Amacr have been shown to be associated with disease states. Amino acid sequence alignment of Amacrs and its homologues from various species revealed 26 conserved protic residues, assumed to be potential candidates as catalytic residues. Amacr from Mycobacterium tuberculosis (MCR) was taken as a representative of the racemases. To determine their importance for efficient catalysis, each of these 26 protic residues of MCR was mutated into an alanine, respectively, and the mutated variants were overexpressed in Escherichia coli. It was found that four variants (R91A, H126A, D156A, and E241A) were properly folded but had much decreased catalytic efficiency. Apparently, Arg91, His126, Asp156, and Glu241 are important catalytic residues of MCR. The importance of these residues for catalysis can be rationalized by the 1.8 A resolution crystal structure of MCR, which shows that the catalytic site is at the interface between the large and small domain of two different subunits of the dimeric enzyme. This crystal structure is the first structure of a complete enzyme of the bile acid synthesis pathway. It shows that MCR has unique structural features, not seen in the structures of the sequence related formyl-CoA transferases, suggesting that the family III CoA transferases can be subdivided in at least two classes, being racemases and CoA transferases.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. The substrate molecules of Amacr. The covalent structures of pristanoyl-CoA, 3,7,12-trihydroxycoprostanoyl-CoA, and ibuprofenoyl-CoA are shown. Amacr interconverts the chirality of the -carbon of the acyl moiety.
Figure 8.
FIG. 8. The MCR dimer. Subunit A is shown in green, and subunit B is shown in orange. The side chains of the mutated residues (see "Discussion") of subunit A are highlighted and labeled as follows: cyan, Ile^56 ("I"); cyan, Met111 ("M"); red, Arg52 ("R"); brown, Glu82 ("E"); purple, Asp190 ("D"); black, Cys297 ("C"); gray, His312 ("H"). The mutated residues near the active site are shown in atom coloring mode: Arg91 ("R"), His126 ("H"), Asp156 ("D"), Glu241 ("E"), as well as the acetyl-CoA molecule of the superimposed E. coli YfdW structure.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 12611-12620) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19156321 D.J.Darley, D.S.Butler, S.J.Prideaux, T.W.Thornton, A.D.Wilson, T.J.Woodman, M.D.Threadgill, and M.D.Lloyd (2009).
Synthesis and use of isotope-labelled substrates for a mechanistic study on human alpha-methylacyl-CoA racemase 1A (AMACR; P504S).
  Org Biomol Chem, 7, 543-552.  
18854979 F.G.Barcellos, J.S.Batista, P.Menna, and M.Hungria (2009).
Genetic differences between Bradyrhizobium japonicum variant strains contrasting in N(2)-fixation efficiency revealed by representational difference analysis.
  Arch Microbiol, 191, 113-122.  
18245280 C.G.Toyota, C.L.Berthold, A.Gruez, S.Jónsson, Y.Lindqvist, C.Cambillau, and N.G.Richards (2008).
Differential substrate specificity and kinetic behavior of Escherichia coli YfdW and Oxalobacter formigenes formyl coenzyme A transferase.
  J Bacteriol, 190, 2556-2564.
PDB codes: 2vjp 2vjq
18636118 D.Cruz, A.D.Watson, C.S.Miller, D.Montoya, M.T.Ochoa, P.A.Sieling, M.A.Gutierrez, M.Navab, S.T.Reddy, J.L.Witztum, A.M.Fogelman, T.H.Rea, D.Eisenberg, J.Berliner, and R.L.Modlin (2008).
Host-derived oxidized phospholipids and HDL regulate innate immunity in human leprosy.
  J Clin Invest, 118, 2917-2928.  
18279392 M.D.Lloyd, D.J.Darley, A.S.Wierzbicki, and M.D.Threadgill (2008).
Alpha-methylacyl-CoA racemase--an 'obscure' metabolic enzyme takes centre stage.
  FEBS J, 275, 1089-1102.  
18820059 Q.Arenskötter, J.Heller, D.Dietz, M.Arenskötter, and A.Steinbüchel (2008).
Cloning and characterization of alpha-methylacyl coenzyme A racemase from Gordonia polyisoprenivorans VH2.
  Appl Environ Microbiol, 74, 7085-7089.  
16755588 K.S.Lee, S.M.Park, K.H.Rhee, W.G.Bang, K.Y.Hwang, and Y.M.Chi (2006).
Crystal structure of fatty acid-CoA racemase from Mycobacterium tuberculosis H37Rv.
  Proteins, 64, 817-822.
PDB code: 2g04
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.