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PDBsum entry 1mns

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protein ligands metals links
Racemase PDB id
1mns
Jmol
Contents
Protein chain
357 a.a. *
Ligands
APG
Metals
_MG
Waters ×209
* Residue conservation analysis
PDB id:
1mns
Name: Racemase
Title: On the role of lysine 166 in the mechanism of mandelate race pseudomonas putida: mechanistic and crystallographic eviden stereospecific alkylation by (r)-alpha-phenylglycidate
Structure: Mandelate racemase. Chain: a. Engineered: yes
Source: Pseudomonas putida. Organism_taxid: 303
Biol. unit: Octamer (from PQS)
Resolution:
2.00Å     R-factor:   0.153    
Authors: D.J.Neidhart,J.A.Landro,J.W.Kozarich
Key ref:
J.A.Landro et al. (1994). The role of lysine 166 in the mechanism of mandelate racemase from Pseudomonas putida: mechanistic and crystallographic evidence for stereospecific alkylation by (R)-alpha-phenylglycidate. Biochemistry, 33, 635-643. PubMed id: 8292591 DOI: 10.1021/bi00169a003
Date:
06-Jul-93     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P11444  (MANR_PSEPU) -  Mandelate racemase
Seq:
Struc:
359 a.a.
357 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.1.2.2  - Mandelate racemase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (S)-mandelate = (R)-mandelate
(S)-mandelate
Bound ligand (Het Group name = APG)
matches with 91.67% similarity
= (R)-mandelate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi00169a003 Biochemistry 33:635-643 (1994)
PubMed id: 8292591  
 
 
The role of lysine 166 in the mechanism of mandelate racemase from Pseudomonas putida: mechanistic and crystallographic evidence for stereospecific alkylation by (R)-alpha-phenylglycidate.
J.A.Landro, J.A.Gerlt, J.W.Kozarich, C.W.Koo, V.J.Shah, G.L.Kenyon, D.J.Neidhart, S.Fujita, G.A.Petsko.
 
  ABSTRACT  
 
The mechanism of irreversible inactivation of mandelate racemase (MR) from Pseudomonas putida by alpha-phenylglycidate (alpha PGA) has been investigated stereochemically and crystallographically. The (R) and (S) enantiomers of alpha PGA were synthesized in high enantiomeric excess (81% ee and 83% ee, respectively) using Sharpless epoxidation chemistry. (R)-alpha PGA was determined to be a stereospecific and stoichiometric irreversible inactivator of MR. (S)-alpha PGA does not inactivate MR and appears to bind noncovalently to the active site of MR with less affinity than that of (R)-alpha PGA. The X-ray crystal structure (2.0-A resolution) of MR inactivated by (R)-alpha PGA revealed the presence of a covalent adduct formed by nucleophilic attack of the epsilon-amino group of Lys 166 on the distal carbon on the epoxide ring of (R)-alpha PGA. The proximity of the alpha-proton of (S)-mandelate to Lys 166 [configurationally equivalent to (R)-alpha PGA] was corroborated by the crystal structure (2.1-A resolution) of MR complexed with the substrate analog/competitive inhibitor, (S)-atrolactate [(S)-alpha-methylmandelate]. These results support the proposal that Lys 166 is the polyvalent acid/base responsible for proton transfers on the (S) face of mandelate. In addition, the high-resolution structures also provide insight into the probable interactions of mandelate with the essential Mg2+ and functional groups in the active site.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18646866 B.A.Robertson, W.H.Johnson, H.H.Lo, and C.P.Whitman (2008).
Inactivation of Cg10062, a cis-3-chloroacrylic acid dehalogenase homologue in Corynebacterium glutamicum, by (R)- and (S)-oxirane-2-carboxylate: analysis and implications.
  Biochemistry, 47, 8796-8803.  
18493744 M.Dambeck, and J.Soppa (2008).
Characterization of a Haloferax volcanii member of the enolase superfamily: deletion mutant construction, expression analysis, and transcriptome comparison.
  Arch Microbiol, 190, 341-353.  
18214979 M.Hayashida, S.H.Kim, K.Takeda, T.Hisano, and K.Miki (2008).
Crystal structure of N-acylamino acid racemase from Thermus thermophilus HB8.
  Proteins, 71, 519-523.
PDB code: 2zc8
15146493 E.C.Meng, B.J.Polacco, and P.C.Babbitt (2004).
Superfamily active site templates.
  Proteins, 55, 962-976.  
12952952 E.L.Wise, D.E.Graham, R.H.White, and I.Rayment (2003).
The structural determination of phosphosulfolactate synthase from Methanococcus jannaschii at 1.7-A resolution: an enolase that is not an enolase.
  J Biol Chem, 278, 45858-45863.
PDB code: 1qwg
11900548 M.St Maurice, and S.L.Bearne (2002).
Kinetics and thermodynamics of mandelate racemase catalysis.
  Biochemistry, 41, 4048-4058.  
11395407 J.A.Gerlt, and P.C.Babbitt (2001).
Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.
  Annu Rev Biochem, 70, 209-246.  
11738171 J.P.Richard, and T.L.Amyes (2001).
Proton transfer at carbon.
  Curr Opin Chem Biol, 5, 626-633.  
10769114 A.M.Gulick, B.K.Hubbard, J.A.Gerlt, and I.Rayment (2000).
Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli.
  Biochemistry, 39, 4590-4602.
PDB codes: 1ec7 1ec8 1ec9 1ecq
10924740 M.Paetzel, R.E.Dalbey, and N.C.Strynadka (2000).
The structure and mechanism of bacterial type I signal peptidases. A novel antibiotic target.
  Pharmacol Ther, 87, 27-49.  
11063568 M.St Maurice, and S.L.Bearne (2000).
Reaction intermediate analogues for mandelate racemase: interaction between Asn 197 and the alpha-hydroxyl of the substrate promotes catalysis.
  Biochemistry, 39, 13324-13335.  
10978150 T.B.Thompson, J.B.Garrett, E.A.Taylor, R.Meganathan, J.A.Gerlt, and I.Rayment (2000).
Evolution of enzymatic activity in the enolase superfamily: structure of o-succinylbenzoate synthase from Escherichia coli in complex with Mg2+ and o-succinylbenzoate.
  Biochemistry, 39, 10662-10676.
PDB codes: 1fhu 1fhv
10194342 D.R.Palmer, J.B.Garrett, V.Sharma, R.Meganathan, P.C.Babbitt, and J.A.Gerlt (1999).
Unexpected divergence of enzyme function and sequence: "N-acylamino acid racemase" is o-succinylbenzoate synthase.
  Biochemistry, 38, 4252-4258.  
10336378 U.Schell, S.Helin, T.Kajander, M.Schlömann, and A.Goldman (1999).
Structural basis for the activity of two muconate cycloisomerase variants toward substituted muconates.
  Proteins, 34, 125-136.
PDB codes: 2muc 3muc
9890975 Y.R.Chen, F.W.Larimer, E.H.Serpersu, and F.C.Hartman (1999).
Identification of a catalytic aspartyl residue of D-ribulose 5-phosphate 3-epimerase by site-directed mutagenesis.
  J Biol Chem, 274, 2132-2136.  
9772161 A.M.Gulick, D.R.Palmer, P.C.Babbitt, J.A.Gerlt, and I.Rayment (1998).
Evolution of enzymatic activities in the enolase superfamily: crystal structure of (D)-glucarate dehydratase from Pseudomonas putida.
  Biochemistry, 37, 14358-14368.
PDB code: 1bqg
9772160 D.R.Palmer, B.K.Hubbard, and J.A.Gerlt (1998).
Evolution of enzymatic activities in the enolase superfamily: partitioning of reactive intermediates by (D)-glucarate dehydratase from Pseudomonas putida.
  Biochemistry, 37, 14350-14357.  
9748211 W.W.Cleland, P.A.Frey, and J.A.Gerlt (1998).
The low barrier hydrogen bond in enzymatic catalysis.
  J Biol Chem, 273, 25529-25532.  
9348662 C.L.Perrin, and J.B.Nielson (1997).
"Strong" hydrogen bonds in chemistry and biology.
  Annu Rev Phys Chem, 48, 511-544.  
9125531 L.E.Rabow, and Y.W.Kow (1997).
Mechanism of action of base release by Escherichia coli Fpg protein: role of lysine 155 in catalysis.
  Biochemistry, 36, 5084-5096.  
9048548 S.L.Bearne, and R.Wolfenden (1997).
Mandelate racemase in pieces: effective concentrations of enzyme functional groups in the transition state.
  Biochemistry, 36, 1646-1656.  
9230045 W.Shi, J.Dunbar, M.M.Jayasekera, R.E.Viola, and G.K.Farber (1997).
The structure of L-aspartate ammonia-lyase from Escherichia coli.
  Biochemistry, 36, 9136-9144.
PDB code: 1jsw
8555196 L.A.Highbarger, J.A.Gerlt, and G.L.Kenyon (1996).
Mechanism of the reaction catalyzed by acetoacetate decarboxylase. Importance of lysine 116 in determining the pKa of active-site lysine 115.
  Biochemistry, 35, 41-46.  
8987982 P.C.Babbitt, M.S.Hasson, J.E.Wedekind, D.R.Palmer, W.C.Barrett, G.H.Reed, I.Rayment, D.Ringe, G.L.Kenyon, and J.A.Gerlt (1996).
The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids.
  Biochemistry, 35, 16489-16501.  
8639525 S.L.Schafer, W.C.Barrett, A.T.Kallarakal, B.Mitra, J.W.Kozarich, J.A.Gerlt, J.G.Clifton, G.A.Petsko, and G.L.Kenyon (1996).
Mechanism of the reaction catalyzed by mandelate racemase: structure and mechanistic properties of the D270N mutant.
  Biochemistry, 35, 5662-5669.
PDB code: 1mra
7846026 V.N.Maiorov, and G.M.Crippen (1994).
Learning about protein folding via potential functions.
  Proteins, 20, 167-173.  
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.