PDBsum entry 1jfl

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Isomerase PDB id
Protein chains
228 a.a. *
Waters ×315
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure determination of aspartate racemase from a
Structure: Aspartate racemase. Chain: a, b. Engineered: yes
Source: Pyrococcus horikoshii. Organism_taxid: 70601. Strain: ot3. Gene: ph0670. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
1.90Å     R-factor:   0.194     R-free:   0.222
Authors: L.J.Liu,K.Iwata,A.Kita,Y.Kawarabayasi,M.Yohda,K.Miki
Key ref:
L.Liu et al. (2002). Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and its implications for molecular mechanism of PLP-independent racemization. J Mol Biol, 319, 479-489. PubMed id: 12051922 DOI: 10.1016/S0022-2836(02)00296-6
21-Jun-01     Release date:   05-Jun-02    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
O58403  (O58403_PYRHO) -  228aa long hypothetical aspartate racemase
228 a.a.
228 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     racemase and epimerase activity, acting on amino acids and derivatives     2 terms  


DOI no: 10.1016/S0022-2836(02)00296-6 J Mol Biol 319:479-489 (2002)
PubMed id: 12051922  
Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and its implications for molecular mechanism of PLP-independent racemization.
L.Liu, K.Iwata, A.Kita, Y.Kawarabayasi, M.Yohda, K.Miki.
There exists a d-enantiomer of aspartic acid in lactic acid bacteria and several hyperthermophilic archaea, which is biosynthesized from the l-enantiomer by aspartate racemase. Aspartate racemase is a representative pyridoxal 5'-phosphate (PLP)-independent amino acid racemase. The "two-base" catalytic mechanism has been proposed for this type of racemase, in which a pair of cysteine residues are utilized as the conjugated catalytic acid and base. We have determined the three-dimensional structure of aspartate racemase from the hyperthermophilic archaeum Pyrococcus horikoshii OT3 at 1.9 A resolution by X-ray crystallography and refined it to a crystallographic R factor of 19.4% (R(free) of 22.2%). This is the first structure reported for aspartate racemase, indeed for any amino acid racemase from archaea. The crystal structure revealed that this enzyme forms a stable dimeric structure with a strong three-layered inter-subunit interaction, and that its subunit consists of two structurally homologous alpha/beta domains, each containing a four-stranded parallel beta-sheet flanked by six alpha-helices. Two strictly conserved cysteine residues (Cys82 and Cys194), which have been shown biochemically to act as catalytic acid and base, are located on both sides of a cleft between the two domains. The spatial arrangement of these two cysteine residues supports the "two-base" mechanism but disproves the previous hypothesis that the active site of aspartate racemase is located at the dimeric interface. The structure revealed a unique pseudo mirror-symmetry in the spatial arrangement of the residues around the active site, which may explain the molecular recognition mechanism of the mirror-symmetric aspartate enantiomers by the non-mirror-symmetric aspartate racemase.
  Selected figure(s)  
Figure 2.
Figure 2. A stereoview of the superimposition of the overall structures of P. horikoshii OT3 AspR (blue) and A. pyrophilus GluR (red). The dimerization regions of both enzymes are indicated by the broken-line ellipses in the same colors as their backbones.
Figure 4.
Figure 4. The dimeric structure of P. horikoshii OT3 AspR. A ribbon diagram of the dimer, viewed (a) along the NCS twofold axis (indicated as a brown dot) and (b) perpendicular to the NCS twofold axis (indicated as a vertical, broken brown line). The regions of active sites are indicated by orange circles. Three parts of secondary structure elements that participate in the inter-subunit interaction are labeled. The double-sized inter-subunit b-sheet is indicated by a blue arc in (b). The inter-subunit disulfide bond, b-sheet and a-helix contact in the dimerization interface are shown in (c), (d) and (e), respectively. Relevant residues are labeled and hydrogen bonds are depicted by red broken lines. Two conformations of the disulfide bond are shown in (c), and five ordered water molecules are shown as green balls in (d) and (e). Contacts between a-helices are indicated by red broken-line ellipses in (e).
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 319, 479-489) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20564572 D.Matsui, and T.Oikawa (2010).
Detection and function of the intramolecular disulfide bond in arginine racemase: an enzyme with broad substrate specificity.
  Chem Biodivers, 7, 1591-1602.  
20361049 J.O.Wrabl, and V.J.Hilser (2010).
Investigating homology between proteins using energetic profiles.
  PLoS Comput Biol, 6, e1000722.  
19031045 C.Weiss, A.Bonshtien, O.Farchi-Pisanty, A.Vitlin, and A.Azem (2009).
Cpn20: Siamese twins of the chaperonin world.
  Plant Mol Biol, 69, 227-238.  
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.  
  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.  
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
16510449 S.Bellais, M.Arthur, L.Dubost, J.E.Hugonnet, L.Gutmann, J.van Heijenoort, R.Legrand, J.P.Brouard, L.Rice, and J.L.Mainardi (2006).
Aslfm, the D-aspartate ligase responsible for the addition of D-aspartic acid onto the peptidoglycan precursor of Enterococcus faecium.
  J Biol Chem, 281, 11586-11594.  
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.  
16021630 D.Liger, S.Quevillon-Cheruel, I.Sorel, M.Bremang, K.Blondeau, I.Aboulfath, J.Janin, H.van Tilbeurgh, and N.Leulliot (2005).
Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily.
  Proteins, 60, 778-786.
PDB code: 1ym5
  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.  
15632186 K.Savolainen, P.Bhaumik, W.Schmitz, T.J.Kotti, E.Conzelmann, R.K.Wierenga, and J.K.Hiltunen (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.
PDB code: 1x74
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
15606767 T.Yamashita, M.Ashiuchi, K.Ohnishi, S.Kato, S.Nagata, and H.Misono (2004).
Molecular identification of monomeric aspartate racemase from Bifidobacterium bifidum.
  Eur J Biochem, 271, 4798-4803.  
  16233494 T.Yoshimura, and N.Esak (2003).
Amino acid racemases: functions and mechanisms.
  J Biosci Bioeng, 96, 103-109.  
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.