1jfl: Difference between revisions

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CRYSTAL STRUCTURE DETERMINATION OF ASPARTATE RACEMASE FROM AN ARCHAEA

OverviewOverview

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 StructureAbout 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.

ReferenceReference

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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 '''CRYSTAL STRUCTURE DETERMINATION OF ASPARTATE RACEMASE FROM AN ARCHAEA'''<br />
 ==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.
+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==
-JFL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Active as [http://en.wikipedia.org/wiki/Aspartate_racemase Aspartate racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.13 5.1.1.13] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1JFL OCA].
+JFL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Active as [http://en.wikipedia.org/wiki/Aspartate_racemase Aspartate racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.13 5.1.1.13] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JFL OCA].
 ==Reference==
@@ Line 17: / Line 17: @@
 [[Category: Kawarabayasi, Y.]]
 [[Category: Kita, A.]]
-[[Category: Liu, L.J.]]
+[[Category: Liu, L J.]]
 [[Category: Miki, K.]]
 [[Category: Yohda, M.]]
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 [[Category: homologous domains]]
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