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PDBsum entry 1b73

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protein links
Isomerase PDB id
1b73
Jmol
Contents
Protein chain
252 a.a. *
Waters ×107
* Residue conservation analysis
PDB id:
1b73
Name: Isomerase
Title: Glutamate racemase from aquifex pyrophilus
Structure: Glutamate racemase. Chain: a. Ec: 5.1.1.3
Source: Aquifex pyrophilus. Organism_taxid: 2714
Biol. unit: Dimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.229     R-free:   0.284
Authors: K.Y.Hwang,C.S.Cho,S.S.Kim,Y.G.Yu,Y.Cho
Key ref:
K.Y.Hwang et al. (1999). Structure and mechanism of glutamate racemase from Aquifex pyrophilus. Nat Struct Biol, 6, 422-426. PubMed id: 10331867 DOI: 10.1038/8223
Date:
26-Jan-99     Release date:   28-Jan-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P56868  (MURI_AQUPY) -  Glutamate racemase
Seq:
Struc:
254 a.a.
252 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.5.1.1.3  - Glutamate racemase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-glutamate = D-glutamate
L-glutamate
= D-glutamate
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   5 terms 
  Biochemical function     isomerase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1038/8223 Nat Struct Biol 6:422-426 (1999)
PubMed id: 10331867  
 
 
Structure and mechanism of glutamate racemase from Aquifex pyrophilus.
K.Y.Hwang, C.S.Cho, S.S.Kim, H.C.Sung, Y.G.Yu, Y.Cho.
 
  ABSTRACT  
 
Glutamate racemase (MurI) is responsible for the synthesis of D-glutamate, an essential building block of the peptidoglycan layer in bacterial cell walls. The crystal structure of glutamate racemase from Aquifex pyrophilus, determined at 2.3 A resolution, reveals that the enzyme forms a dimer and each monomer consists of two alpha/beta fold domains, a unique structure that has not been observed in other racemases or members of an enolase superfamily. A substrate analog, D-glutamine, binds to the deep pocket formed by conserved residues from two monomers. The structural and mutational analyses allow us to propose a mechanism of metal cofactor-independent glutamate racemase in which two cysteine residues are involved in catalysis.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. a, A schematic ribbon diagram of the overall structure of a MurI monomer. The N- and C-termini of the protein are labeled, and certain helices are numbered. Each domain is shown in a different color, blue and purple. D-Gln is shown in yellow. b, A stereo diagram of a C trace of a MurI structure in the same orientation as in (a). Every 30^th residue is labeled. c, Secondary structures of MurI as analyzed by DSSP^35 and the sequences of MurI: (row 1) A. pyrophilus MurI; (row 2) H. pyroli MurI. The strictly conserved residues in 10 different MurI sequences are shown in red (see text), and the identical residues in two MurIs from A. pyrophilus and H. pyroli are boxed in yellow.
Figure 3.
Figure 3. a, A 2F[o] - F[c] map showing the active-site region calculated at 2.3 Å resolution. The map is contoured at 1 , with the final model displayed for comparison. b, A stereo diagram of an active-site region in MurI. D-Gln and two catalytic cysteines are shown in yellow, and neighboring residues are shown in cyan. Residues from the other monomer are in red. The glycine-rich loop is shown in green. c, Proposed racemization mechanism of glutamate racemase. The mechanism shown implies a two-base mechanism with base/acid in the active site. The racemization of D-Glu by MurI may proceed by (i) deprotonation of the C proton by Cys 70, (ii) formation of a carbanion intermediate and (iii) reprotonation on the opposite side of the -proton to produce the L-Glu, or reprotonation on the original side of the carbanion to produce D-Glu. Alternatively, it is possible that the racemization reaction may proceed by a concerted mechanism in which a penta-coordinated carbon is formed in the transition state. The intermediate structure is shown within the dashed lines to indicate its hypothetical character. The residues that may interact with the main-chain atoms of substrate (postulated from modeling study) are not shown, but are described in the text.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 422-426) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21161322 F.Cava, H.Lam, M.A.de Pedro, and M.K.Waldor (2011).
Emerging knowledge of regulatory roles of D-amino acids in bacteria.
  Cell Mol Life Sci, 68, 817-831.  
20361049 J.O.Wrabl, and V.J.Hilser (2010).
Investigating homology between proteins using energetic profiles.
  PLoS Comput Biol, 6, e1000722.  
20135034 L.S.Wong, K.Okrasa, and J.Micklefield (2010).
Site-selective immobilisation of functional enzymes on to polystyrene nanoparticles.
  Org Biomol Chem, 8, 782-787.  
19309142 M.A.Spies, J.G.Reese, D.Dodd, K.L.Pankow, S.R.Blanke, and J.Baudry (2009).
Determinants of catalytic power and ligand binding in glutamate racemase.
  J Am Chem Soc, 131, 5274-5284.  
17847084 A.Ohtaki, Y.Nakano, R.Iizuka, T.Arakawa, K.Yamada, M.Odaka, and M.Yohda (2008).
Structure of aspartate racemase complexed with a dual substrate analogue, citric acid, and implications for the reaction mechanism.
  Proteins, 70, 1167-1174.
PDB code: 2dx7
17671981 A.Sánchez-Flores, E.Pérez-Rueda, and L.Segovia (2008).
Protein homology detection and fold inference through multiple alignment entropy profiles.
  Proteins, 70, 248-256.  
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.  
  18607088 M.Nakasako, R.Obata, R.Okubo, S.Nakayama, K.Miyamoto, and H.Ohta (2008).
Crystallization and preliminary X-ray diffraction experiments of arylmalonate decarboxylase from Alcaligenes bronchisepticus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 610-613.  
17496086 D.Dodd, J.G.Reese, C.R.Louer, J.D.Ballard, M.A.Spies, and S.R.Blanke (2007).
Functional comparison of the two Bacillus anthracis glutamate racemases.
  J Bacteriol, 189, 5265-5275.  
17610893 M.May, S.Mehboob, D.C.Mulhearn, Z.Wang, H.Yu, G.R.Thatcher, B.D.Santarsiero, M.E.Johnson, and A.D.Mesecar (2007).
Structural and functional analysis of two glutamate racemase isozymes from Bacillus anthracis and implications for inhibitor design.
  J Mol Biol, 371, 1219-1237.
PDB codes: 2dwu 2gzm
16446443 A.Buschiazzo, M.Goytia, F.Schaeffer, W.Degrave, W.Shepard, C.Grégoire, N.Chamond, A.Cosson, A.Berneman, N.Coatnoan, P.M.Alzari, and P.Minoprio (2006).
Crystal structure, catalytic mechanism, and mitogenic properties of Trypanosoma cruzi proline racemase.
  Proc Natl Acad Sci U S A, 103, 1705-1710.
PDB codes: 1w61 1w62
16723397 B.Pillai, M.M.Cherney, C.M.Diaper, A.Sutherland, J.S.Blanchard, J.C.Vederas, and M.N.James (2006).
Structural insights into stereochemical inversion by diaminopimelate epimerase: an antibacterial drug target.
  Proc Natl Acad Sci U S A, 103, 8668-8673.
PDB codes: 2gke 2gkj
17132860 S.Martínez-Rodríguez, M.Andújar-Sánchez, J.L.Neira, J.M.Clemente-Jiménez, V.Jara-Pérez, F.Rodríguez-Vico, and F.J.Las Heras-Vázquez (2006).
Site-directed mutagenesis indicates an important role of cysteines 76 and 181 in the catalysis of hydantoin racemase from Sinorhizobium meliloti.
  Protein Sci, 15, 2729-2738.  
16705641 T.Yoshida, T.Seko, O.Okada, K.Iwata, L.Liu, K.Miki, and M.Yohda (2006).
Roles of conserved basic amino acid residues and activation mechanism of the hyperthermophilic aspartate racemase at high temperature.
  Proteins, 64, 502-512.  
16327902 C.M.Diaper, A.Sutherland, B.Pillai, M.N.James, P.Semchuk, J.S.Blanchard, and J.C.Vederas (2005).
The stereoselective synthesis of aziridine analogues of diaminopimelic acid (DAP) and their interaction with dap epimerase.
  Org Biomol Chem, 3, 4402-4411.  
15739204 J.Ko, L.F.Murga, P.André, H.Yang, M.J.Ondrechen, R.J.Williams, A.Agunwamba, and D.E.Budil (2005).
Statistical criteria for the identification of protein active sites using Theoretical Microscopic Titration Curves.
  Proteins, 59, 183-195.  
  16510993 K.S.Lee, S.M.Park, K.Y.Hwang, and Y.M.Chi (2005).
Crystallization and preliminary X-ray crystallographic studies of glutamate racemase from Lactobacillus fermenti.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 199-201.  
16271894 S.N.Ruzheinikov, M.A.Taal, S.E.Sedelnikova, P.J.Baker, and D.W.Rice (2005).
Substrate-induced conformational changes in Bacillus subtilis glutamate racemase and their implications for drug discovery.
  Structure, 13, 1707-1713.
PDB code: 1zuw
15700067 Y.Ijima, K.Matoishi, Y.Terao, N.Doi, H.Yanagawa, and H.Ohta (2005).
Inversion of enantioselectivity of asymmetric biocatalytic decarboxylation by site-directed mutagenesis based on the reaction mechanism.
  Chem Commun (Camb), (), 877-879.  
15502318 M.A.Taal, S.E.Sedelnikova, S.N.Ruzheinikov, P.J.Baker, and D.W.Rice (2004).
Expression, purification and preliminary X-ray analysis of crystals of Bacillus subtilis glutamate racemase.
  Acta Crystallogr D Biol Crystallogr, 60, 2031-2034.  
14499611 R.G.Zhang, C.E.Andersson, T.Skarina, E.Evdokimova, A.M.Edwards, A.Joachimiak, A.Savchenko, and S.L.Mowbray (2003).
The 2.2 A resolution structure of RpiB/AlsB from Escherichia coli illustrates a new approach to the ribose-5-phosphate isomerase reaction.
  J Mol Biol, 332, 1083-1094.
PDB code: 1nn4
  16233494 T.Yoshimura, and N.Esak (2003).
Amino acid racemases: functions and mechanisms.
  J Biosci Bioeng, 96, 103-109.  
11738171 J.P.Richard, and T.L.Amyes (2001).
Proton transfer at carbon.
  Curr Opin Chem Biol, 5, 626-633.  
11371180 S.Glavas, and M.E.Tanner (2001).
Active site residues of glutamate racemase.
  Biochemistry, 40, 6199-6204.  
10508663 T.L.Born, and J.S.Blanchard (1999).
Structure/function studies on enzymes in the diaminopimelate pathway of bacterial cell wall biosynthesis.
  Curr Opin Chem Biol, 3, 607-613.  
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.