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PDBsum entry 2sfp

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protein ligands Protein-protein interface(s) links
Racemase PDB id
2sfp
Jmol
Contents
Protein chains
379 a.a. *
Ligands
PLP ×2
PPI ×2
Waters ×207
* Residue conservation analysis
PDB id:
2sfp
Name: Racemase
Title: Alanine racemase with bound propionate inhibitor
Structure: Protein (alanine racemase). Chain: a, b. Engineered: yes. Other_details: pyridoxal phosphate cofactor in aldimine lin lys39. Carboxylated lys129
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Strain: ifo 12550. Expressed in: escherichia coli str. K12 substr. W3110. Expression_system_taxid: 316407.
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
1.90Å     R-factor:   0.205     R-free:   0.259
Authors: A.A.Morollo,G.A.Petsko,D.Ringe
Key ref:
A.A.Morollo et al. (1999). Structure of a Michaelis complex analogue: propionate binds in the substrate carboxylate site of alanine racemase. Biochemistry, 38, 3293-3301. PubMed id: 10079072 DOI: 10.1021/bi9822729
Date:
16-Feb-99     Release date:   24-Feb-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P10724  (ALR_GEOSE) -  Alanine racemase
Seq:
Struc:
388 a.a.
379 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.5.1.1.1  - Alanine racemase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-alanine = D-alanine
L-alanine
Bound ligand (Het Group name = PPI)
matches with 83.33% similarity
= D-alanine
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLP) matches with 93.75% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     alanine metabolic process   2 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi9822729 Biochemistry 38:3293-3301 (1999)
PubMed id: 10079072  
 
 
Structure of a Michaelis complex analogue: propionate binds in the substrate carboxylate site of alanine racemase.
A.A.Morollo, G.A.Petsko, D.Ringe.
 
  ABSTRACT  
 
The structure of alanine racemase from Bacillus stearothermophilus with the inhibitor propionate bound in the active site was determined by X-ray crystallography to a resolution of 1.9 A. The enzyme is a homodimer in solution and crystallizes with a dimer in the asymmetric unit. Both active sites contain a pyridoxal 5'-phosphate (PLP) molecule in aldimine linkage to Lys39 as a protonated Schiff base, and the pH-independence of UV-visible absorption spectra suggests that the protonated PLP-Lys39 Schiff base is the reactive form of the enzyme. The carboxylate group of propionate bound in the active site makes numerous interactions with active-site residues, defining the substrate binding site of the enzyme. The propionate-bound structure therefore approximates features of the Michaelis complex formed between alanine racemase and its amino acid substrate. The structure also provides evidence for the existence of a carbamate formed on the side-chain amino group of Lys129, stabilized by interactions with one of the residues interacting with the carboxylate group of propionate, Arg136. We propose that this novel interaction influences both substrate binding and catalysis by precisely positioning Arg136 and modulating its charge.
 

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
22194336 E.R.Scaletti, S.R.Luckner, and K.L.Krause (2012).
Structural features and kinetic characterization of alanine racemase from Staphylococcus aureus (Mu50).
  Acta Crystallogr D Biol Crystallogr, 68, 82-92.
PDB code: 4a3q
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.  
19695097 R.M.Couñago, M.Davlieva, U.Strych, R.E.Hill, and K.L.Krause (2009).
Biochemical and structural characterization of alanine racemase from Bacillus anthracis (Ames).
  BMC Struct Biol, 9, 53.
PDB code: 3ha1
18434499 D.Wu, T.Hu, L.Zhang, J.Chen, J.Du, J.Ding, H.Jiang, and X.Shen (2008).
Residues Asp164 and Glu165 at the substrate entryway function potently in substrate orientation of alanine racemase from E. coli: Enzymatic characterization with crystal structure analysis.
  Protein Sci, 17, 1066-1076.
PDB codes: 2rjg 2rjh 3b8t 3b8u 3b8v 3b8w
18266853 H.Barreteau, A.Kovac, A.Boniface, M.Sova, S.Gobec, and D.Blanot (2008).
Cytoplasmic steps of peptidoglycan biosynthesis.
  FEMS Microbiol Rev, 32, 168-207.  
18508763 T.Hu, D.Wu, J.Chen, J.Ding, H.Jiang, and X.Shen (2008).
The catalytic intermediate stabilized by a "down" active site loop for diaminopimelate decarboxylase from Helicobacter pylori. Enzymatic characterization with crystal structure analysis.
  J Biol Chem, 283, 21284-21293.  
16121396 J.Li, J.B.Cross, T.Vreven, S.O.Meroueh, S.Mobashery, and H.B.Schlegel (2005).
Lysine carboxylation in proteins: OXA-10 beta-lactamase.
  Proteins, 61, 246-257.  
15840827 J.Zhang, A.V.Cheltsov, and G.C.Ferreira (2005).
Conversion of 5-aminolevulinate synthase into a more active enzyme by linking the two subunits: spectroscopic and kinetic properties.
  Protein Sci, 14, 1190-1200.  
15302886 M.Noda, Y.Matoba, T.Kumagai, and M.Sugiyama (2004).
Structural evidence that alanine racemase from a D-cycloserine-producing microorganism exhibits resistance to its own product.
  J Biol Chem, 279, 46153-46161.
PDB codes: 1vfh 1vfs 1vft
14517907 G.I.Mustata, T.A.Soares, and J.M.Briggs (2003).
Molecular dynamics studies of alanine racemase: a structural model for drug design.
  Biopolymers, 70, 186-200.  
14674749 P.LeMagueres, H.Im, A.Dvorak, U.Strych, M.Benedik, and K.L.Krause (2003).
Crystal structure at 1.45 A resolution of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms.
  Biochemistry, 42, 14752-14761.
PDB code: 1rcq
  16233494 T.Yoshimura, and N.Esak (2003).
Amino acid racemases: functions and mechanisms.
  J Biosci Bioeng, 96, 103-109.  
11886871 A.Watanabe, T.Yoshimura, B.Mikami, H.Hayashi, H.Kagamiyama, and N.Esaki (2002).
Reaction mechanism of alanine racemase from Bacillus stearothermophilus: x-ray crystallographic studies of the enzyme bound with N-(5'-phosphopyridoxyl)alanine.
  J Biol Chem, 277, 19166-19172.
PDB codes: 1l6f 1l6g
12429091 S.S.Ray, J.B.Bonanno, K.R.Rajashankar, M.G.Pinho, G.He, H.De Lencastre, A.Tomasz, and S.K.Burley (2002).
Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor.
  Structure, 10, 1499-1508.
PDB codes: 1tuf 1twi
12107154 U.Strych, and M.J.Benedik (2002).
Mutant analysis shows that alanine racemases from Pseudomonas aeruginosa and Escherichia coli are dimeric.
  J Bacteriol, 184, 4321-4325.  
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 code is shown on the right.