1jfl
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(New page: 200px<br /><applet load="1jfl" size="450" color="white" frame="true" align="right" spinBox="true" caption="1jfl, resolution 1.90Å" /> '''CRYSTAL STRUCTURE DE...)
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Revision as of 21:26, 24 November 2007
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CRYSTAL STRUCTURE DETERMINATION OF ASPARTATE RACEMASE FROM AN ARCHAEA
Overview
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.
About this Structure
1JFL is a Single protein structure of sequence from Pyrococcus horikoshii. Active as Aspartate racemase, with EC number 5.1.1.13 Full crystallographic information is available from OCA.
Reference
Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and its implications for molecular mechanism of PLP-independent racemization., Liu L, Iwata K, Kita A, Kawarabayasi Y, Yohda M, Miki K, J Mol Biol. 2002 May 31;319(2):479-89. PMID:12051922
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