RACD_PYRHO
ID RACD_PYRHO Reviewed; 228 AA.
AC O58403;
DT 27-MAY-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=Aspartate racemase;
DE EC=5.1.1.13 {ECO:0000269|PubMed:17847084};
GN OrderedLocusNames=PH0670 {ECO:0000312|EMBL:BAA29761.1};
OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS 100139 / OT-3).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=70601 {ECO:0000312|EMBL:BAA29761.1};
RN [1] {ECO:0000312|Proteomes:UP000000752}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
RC {ECO:0000312|Proteomes:UP000000752};
RX PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT "Complete sequence and gene organization of the genome of a hyper-
RT thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL DNA Res. 5:55-76(1998).
RN [2] {ECO:0007744|PDB:1IU9}
RP X-RAY CRYSTALLOGRAPHY (2.04 ANGSTROMS) OF 103-213.
RX PubMed=12297289; DOI=10.1016/s0014-5793(02)03264-7;
RA Liu L., Iwata K., Yohda M., Miki K.;
RT "Structural insight into gene duplication, gene fusion and domain swapping
RT in the evolution of PLP-independent amino acid racemases.";
RL FEBS Lett. 528:114-118(2002).
RN [3] {ECO:0007744|PDB:1JFL}
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS), SUBUNIT, AND DISULFIDE BOND.
RX PubMed=12051922; DOI=10.1016/s0022-2836(02)00296-6;
RA Liu L., Iwata K., Kita A., Kawarabayasi Y., Yohda M., Miki K.;
RT "Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and
RT its implications for molecular mechanism of PLP-independent racemization.";
RL J. Mol. Biol. 319:479-489(2002).
RN [4] {ECO:0007744|PDB:2DX7}
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF MUTANT ALA-82 IN COMPLEX WITH THE
RP SUBSTRATE ANALOG CITRATE, DISULFIDE BOND, ACTIVE SITE, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION, AND MUTAGENESIS OF
RP CYS-82.
RX PubMed=17847084; DOI=10.1002/prot.21528;
RA Ohtaki A., Nakano Y., Iizuka R., Arakawa T., Yamada K., Odaka M., Yohda M.;
RT "Structure of aspartate racemase complexed with a dual substrate analogue,
RT citric acid, and implications for the reaction mechanism.";
RL Proteins 70:1167-1174(2008).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-aspartate = D-aspartate; Xref=Rhea:RHEA:14973,
CC ChEBI:CHEBI:29990, ChEBI:CHEBI:29991; EC=5.1.1.13;
CC Evidence={ECO:0000269|PubMed:17847084};
CC -!- ACTIVITY REGULATION: Weakly inhibited by citrate, but not by
CC asparagine. {ECO:0000269|PubMed:17847084}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.7 mM for L-aspartate {ECO:0000269|PubMed:17847084};
CC -!- SUBUNIT: Homodimer. The existence of the interchain disulfide bond seen
CC in the crystal structures is uncertain, but disulfide bonds have been
CC reported for cytoplasmic proteins from thermophiles.
CC {ECO:0000269|PubMed:12051922, ECO:0000269|PubMed:17847084,
CC ECO:0000305}.
CC -!- SIMILARITY: Belongs to the aspartate/glutamate racemases family.
CC {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; BA000001; BAA29761.1; -; Genomic_DNA.
DR PIR; G71112; G71112.
DR RefSeq; WP_010884762.1; NC_000961.1.
DR PDB; 1IU9; X-ray; 2.04 A; A=103-213.
DR PDB; 1JFL; X-ray; 1.90 A; A/B=1-228.
DR PDB; 2DX7; X-ray; 2.00 A; A/B=1-228.
DR PDBsum; 1IU9; -.
DR PDBsum; 1JFL; -.
DR PDBsum; 2DX7; -.
DR AlphaFoldDB; O58403; -.
DR SMR; O58403; -.
DR STRING; 70601.3257078; -.
DR EnsemblBacteria; BAA29761; BAA29761; BAA29761.
DR GeneID; 1442997; -.
DR KEGG; pho:PH0670; -.
DR eggNOG; arCOG02006; Archaea.
DR OMA; CNTAHFF; -.
DR OrthoDB; 67642at2157; -.
DR BRENDA; 5.1.1.13; 5244.
DR SABIO-RK; O58403; -.
DR EvolutionaryTrace; O58403; -.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0047689; F:aspartate racemase activity; IEA:UniProtKB-EC.
DR GO; GO:0006807; P:nitrogen compound metabolic process; IEA:InterPro.
DR InterPro; IPR015942; Asp/Glu/hydantoin_racemase.
DR InterPro; IPR001920; Asp/Glu_race.
DR InterPro; IPR018187; Asp/Glu_racemase_AS_1.
DR InterPro; IPR004380; Asp_race.
DR PANTHER; PTHR21198:SF7; PTHR21198:SF7; 1.
DR Pfam; PF01177; Asp_Glu_race; 1.
DR SUPFAM; SSF53681; SSF53681; 2.
DR TIGRFAMs; TIGR00035; asp_race; 1.
DR PROSITE; PS00923; ASP_GLU_RACEMASE_1; 1.
DR PROSITE; PS00924; ASP_GLU_RACEMASE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Disulfide bond; Isomerase.
FT CHAIN 1..228
FT /note="Aspartate racemase"
FT /id="PRO_0000433135"
FT ACT_SITE 82
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:17847084"
FT ACT_SITE 194
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:17847084"
FT BINDING 47..49
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:17847084,
FT ECO:0007744|PDB:2DX7"
FT BINDING 83..85
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:17847084,
FT ECO:0007744|PDB:2DX7"
FT BINDING 164
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:17847084,
FT ECO:0007744|PDB:2DX7"
FT DISULFID 73
FT /note="Interchain"
FT /evidence="ECO:0000305|PubMed:17847084,
FT ECO:0007744|PDB:1JFL, ECO:0007744|PDB:2DX7"
FT MUTAGEN 82
FT /note="C->A: Abolishes racemase activity."
FT /evidence="ECO:0000269|PubMed:17847084"
FT STRAND 4..8
FT /evidence="ECO:0007829|PDB:1JFL"
FT HELIX 12..24
FT /evidence="ECO:0007829|PDB:1JFL"
FT HELIX 31..33
FT /evidence="ECO:0007829|PDB:1JFL"
FT STRAND 37..41
FT /evidence="ECO:0007829|PDB:1JFL"
FT HELIX 48..52
FT /evidence="ECO:0007829|PDB:1JFL"
FT HELIX 60..73
FT /evidence="ECO:0007829|PDB:1JFL"
FT STRAND 76..79
FT /evidence="ECO:0007829|PDB:1JFL"
FT HELIX 84..88
FT /evidence="ECO:0007829|PDB:1JFL"
FT HELIX 89..95
FT /evidence="ECO:0007829|PDB:1JFL"
FT HELIX 103..113
FT /evidence="ECO:0007829|PDB:1JFL"
FT STRAND 117..122
FT /evidence="ECO:0007829|PDB:1JFL"
FT HELIX 125..130
FT /evidence="ECO:0007829|PDB:1JFL"
FT HELIX 132..139
FT /evidence="ECO:0007829|PDB:1JFL"
FT STRAND 143..145
FT /evidence="ECO:0007829|PDB:1JFL"
FT HELIX 149..160
FT /evidence="ECO:0007829|PDB:1JFL"
FT HELIX 163..165
FT /evidence="ECO:0007829|PDB:1JFL"
FT HELIX 168..184
FT /evidence="ECO:0007829|PDB:1JFL"
FT STRAND 188..192
FT /evidence="ECO:0007829|PDB:1JFL"
FT HELIX 195..200
FT /evidence="ECO:0007829|PDB:1JFL"
FT HELIX 203..205
FT /evidence="ECO:0007829|PDB:1JFL"
FT HELIX 213..226
FT /evidence="ECO:0007829|PDB:1JFL"
SQ SEQUENCE 228 AA; 25158 MW; DDAA2CBEB39682CF CRC64;
MKTIGILGGM GPLATAELFR RIVIKTPAKR DQEHPKVIIF NNPQIPDRTA YILGKGEDPR
PQLIWTAKRL EECGADFIIM PCNTAHAFVE DIRKAIKIPI ISMIEETAKK VKELGFKKAG
LLATTGTIVS GVYEKEFSKY GVEIMTPTED EQKDVMRGIY EGVKAGNLKL GRELLLKTAK
ILEERGAECI IAGCTEVSVV LKQDDLKVPL IDPMDVIAEV AVKVALEK
