PPAT_RHILO
ID PPAT_RHILO Reviewed; 393 AA.
AC Q988B8; Q2Z2G1;
DT 03-SEP-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2001, sequence version 1.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=Pyridoxamine--pyruvate transaminase;
DE EC=2.6.1.30 {ECO:0000269|PubMed:16545075};
DE AltName: Full=Pyridoxamine-pyruvate aminotransferase {ECO:0000303|PubMed:16545075};
GN Name=ppaT; OrderedLocusNames=mlr6806;
OS Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
OS (Mesorhizobium loti (strain MAFF 303099)).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Phyllobacteriaceae; Mesorhizobium.
OX NCBI_TaxID=266835;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-8, FUNCTION,
RP CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF LYS-197
RP AND CYS-198, AND COFACTOR.
RC STRAIN=LMG 29417 / CECT 9101 / MAFF 303099;
RX PubMed=16545075; DOI=10.1042/bj20060078;
RA Yoshikane Y., Yokochi N., Ohnishi K., Hayashi H., Yagi T.;
RT "Molecular cloning, expression and characterization of pyridoxamine-
RT pyruvate aminotransferase.";
RL Biochem. J. 396:499-507(2006).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LMG 29417 / CECT 9101 / MAFF 303099;
RX PubMed=11214968; DOI=10.1093/dnares/7.6.331;
RA Kaneko T., Nakamura Y., Sato S., Asamizu E., Kato T., Sasamoto S.,
RA Watanabe A., Idesawa K., Ishikawa A., Kawashima K., Kimura T., Kishida Y.,
RA Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Mochizuki Y.,
RA Nakayama S., Nakazaki N., Shimpo S., Sugimoto M., Takeuchi C., Yamada M.,
RA Tabata S.;
RT "Complete genome structure of the nitrogen-fixing symbiotic bacterium
RT Mesorhizobium loti.";
RL DNA Res. 7:331-338(2000).
RN [3] {ECO:0007744|PDB:2Z9U, ECO:0007744|PDB:2Z9V, ECO:0007744|PDB:2Z9W, ECO:0007744|PDB:2Z9X}
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 2-393 IN COMPLEX WITH PYRIDOXAL
RP PHOSPHATE, FUNCTION, COFACTOR, SUBUNIT, AND MUTAGENESIS OF GLU-68 AND
RP ARG-336.
RC STRAIN=LMG 29417 / CECT 9101 / MAFF 303099;
RX PubMed=17989071; DOI=10.1074/jbc.m708061200;
RA Yoshikane Y., Yokochi N., Yamasaki M., Mizutani K., Ohnishi K., Mikami B.,
RA Hayashi H., Yagi T.;
RT "Crystal structure of pyridoxamine-pyruvate aminotransferase from
RT Mesorhizobium loti MAFF303099.";
RL J. Biol. Chem. 283:1120-1127(2008).
CC -!- FUNCTION: Catalyzes a reversible transamination reaction between
CC pyridoxamine and pyruvate to form pyridoxal and L-alanine.
CC {ECO:0000269|PubMed:16545075, ECO:0000269|PubMed:17989071}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=pyridoxamine + pyruvate = L-alanine + pyridoxal;
CC Xref=Rhea:RHEA:12841, ChEBI:CHEBI:15361, ChEBI:CHEBI:17310,
CC ChEBI:CHEBI:57761, ChEBI:CHEBI:57972; EC=2.6.1.30;
CC Evidence={ECO:0000269|PubMed:16545075};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:16545075, ECO:0000269|PubMed:17989071};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.044 mM for pyridoxamine {ECO:0000269|PubMed:16545075};
CC KM=0.059 mM for pyridoxal {ECO:0000269|PubMed:16545075};
CC KM=0.34 mM for pyruvate {ECO:0000269|PubMed:16545075};
CC KM=7.1 mM for 2-oxobutyrate {ECO:0000269|PubMed:16545075};
CC KM=11 mM for L-alanine {ECO:0000269|PubMed:16545075};
CC KM=20 mM for (S)-2-aminobutyrate {ECO:0000269|PubMed:16545075};
CC Note=kcat is 28 sec(-1) for pyridoxamine. kcat is 41 sec(-1) for
CC pyridoxal. kcat is 29 sec(-1) for pyruvate. kcat is 24 sec(-1) for 2-
CC oxobutyrate. kcat is 41 sec(-1) for L-alanine. kcat is 9 sec(-1) for
CC (S)-2-aminobutyrate. {ECO:0000269|PubMed:16545075};
CC pH dependence:
CC Optimum pH is 9.5. {ECO:0000269|PubMed:16545075};
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:17989071}.
CC -!- SIMILARITY: Belongs to the class-V pyridoxal-phosphate-dependent
CC aminotransferase family. {ECO:0000305}.
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DR EMBL; AB195265; BAE48518.1; -; Genomic_DNA.
DR EMBL; BA000012; BAB53032.1; -; Genomic_DNA.
DR PDB; 2Z9U; X-ray; 2.00 A; A/B=2-393.
DR PDB; 2Z9V; X-ray; 1.70 A; A/B=2-393.
DR PDB; 2Z9W; X-ray; 1.70 A; A/B=2-393.
DR PDB; 2Z9X; X-ray; 1.94 A; A/B=2-393.
DR PDBsum; 2Z9U; -.
DR PDBsum; 2Z9V; -.
DR PDBsum; 2Z9W; -.
DR PDBsum; 2Z9X; -.
DR AlphaFoldDB; Q988B8; -.
DR SMR; Q988B8; -.
DR STRING; 266835.14026435; -.
DR EnsemblBacteria; BAB53032; BAB53032; BAB53032.
DR KEGG; mlo:mlr6806; -.
DR eggNOG; COG0075; Bacteria.
DR HOGENOM; CLU_027686_0_1_5; -.
DR OMA; NHTGPRA; -.
DR BioCyc; MetaCyc:MON-13150; -.
DR BRENDA; 2.6.1.30; 15627.
DR SABIO-RK; Q988B8; -.
DR EvolutionaryTrace; Q988B8; -.
DR Proteomes; UP000000552; Chromosome.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IDA:UniProtKB.
DR GO; GO:0047300; F:pyridoxamine-pyruvate transaminase activity; IEA:UniProtKB-EC.
DR GO; GO:0008483; F:transaminase activity; IDA:UniProtKB.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR InterPro; IPR000192; Aminotrans_V_dom.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR InterPro; IPR024169; SP_NH2Trfase/AEP_transaminase.
DR Pfam; PF00266; Aminotran_5; 1.
DR PIRSF; PIRSF000524; SPT; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aminotransferase; Chloride; Direct protein sequencing;
KW Pyridoxal phosphate; Transferase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:16545075"
FT CHAIN 2..393
FT /note="Pyridoxamine--pyruvate transaminase"
FT /id="PRO_0000430257"
FT BINDING 68
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:17989071"
FT BINDING 95
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:17989071"
FT BINDING 146
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:17989071"
FT BINDING 345
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:17989071"
FT MOD_RES 197
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000269|PubMed:17989071"
FT MUTAGEN 68
FT /note="E->A,G: Low but detectable pyridoxamine--pyruvate
FT transaminase activity."
FT /evidence="ECO:0000269|PubMed:17989071"
FT MUTAGEN 197
FT /note="K->L: Loss of function."
FT /evidence="ECO:0000269|PubMed:16545075"
FT MUTAGEN 198
FT /note="C->A: No effect on enzyme activity."
FT /evidence="ECO:0000269|PubMed:16545075"
FT MUTAGEN 336
FT /note="R->A: Strongly decreased affinity for pyruvate."
FT /evidence="ECO:0000269|PubMed:17989071"
FT STRAND 11..13
FT /evidence="ECO:0007829|PDB:2Z9V"
FT STRAND 15..17
FT /evidence="ECO:0007829|PDB:2Z9V"
FT HELIX 23..28
FT /evidence="ECO:0007829|PDB:2Z9V"
FT HELIX 39..55
FT /evidence="ECO:0007829|PDB:2Z9V"
FT STRAND 63..67
FT /evidence="ECO:0007829|PDB:2Z9V"
FT HELIX 70..80
FT /evidence="ECO:0007829|PDB:2Z9V"
FT STRAND 87..93
FT /evidence="ECO:0007829|PDB:2Z9V"
FT HELIX 94..106
FT /evidence="ECO:0007829|PDB:2Z9V"
FT STRAND 110..114
FT /evidence="ECO:0007829|PDB:2Z9V"
FT HELIX 123..132
FT /evidence="ECO:0007829|PDB:2Z9V"
FT STRAND 138..144
FT /evidence="ECO:0007829|PDB:2Z9V"
FT HELIX 146..148
FT /evidence="ECO:0007829|PDB:2Z9V"
FT HELIX 154..163
FT /evidence="ECO:0007829|PDB:2Z9V"
FT STRAND 167..171
FT /evidence="ECO:0007829|PDB:2Z9V"
FT TURN 173..175
FT /evidence="ECO:0007829|PDB:2Z9V"
FT HELIX 183..186
FT /evidence="ECO:0007829|PDB:2Z9V"
FT STRAND 189..193
FT /evidence="ECO:0007829|PDB:2Z9V"
FT STRAND 195..197
FT /evidence="ECO:0007829|PDB:2Z9V"
FT STRAND 206..210
FT /evidence="ECO:0007829|PDB:2Z9V"
FT HELIX 212..219
FT /evidence="ECO:0007829|PDB:2Z9V"
FT HELIX 233..235
FT /evidence="ECO:0007829|PDB:2Z9V"
FT TURN 236..239
FT /evidence="ECO:0007829|PDB:2Z9V"
FT HELIX 251..267
FT /evidence="ECO:0007829|PDB:2Z9V"
FT HELIX 269..289
FT /evidence="ECO:0007829|PDB:2Z9V"
FT STRAND 294..298
FT /evidence="ECO:0007829|PDB:2Z9V"
FT HELIX 299..301
FT /evidence="ECO:0007829|PDB:2Z9V"
FT STRAND 306..310
FT /evidence="ECO:0007829|PDB:2Z9V"
FT HELIX 317..328
FT /evidence="ECO:0007829|PDB:2Z9V"
FT HELIX 337..339
FT /evidence="ECO:0007829|PDB:2Z9V"
FT TURN 340..342
FT /evidence="ECO:0007829|PDB:2Z9V"
FT STRAND 343..347
FT /evidence="ECO:0007829|PDB:2Z9V"
FT HELIX 350..352
FT /evidence="ECO:0007829|PDB:2Z9V"
FT HELIX 355..371
FT /evidence="ECO:0007829|PDB:2Z9V"
FT HELIX 378..392
FT /evidence="ECO:0007829|PDB:2Z9V"
SQ SEQUENCE 393 AA; 41590 MW; EB25E53E28C0AB61 CRC64;
MMRYPEHADP VITLTAGPVN AYPEVLRGLG RTVLYDYDPA FQLLYEKVVD KAQKAMRLSN
KPVILHGEPV LGLEAAAASL ISPDDVVLNL ASGVYGKGFG YWAKRYSPHL LEIEVPYNEA
IDPQAVADML KAHPEITVVS VCHHDTPSGT INPIDAIGAL VSAHGAYLIV DAVSSFGGMK
THPEDCKADI YVTGPNKCLG APPGLTMMGV SERAWAKMKA NPLAPRASML SIVDWENAWS
RDKPFPFTPS VSEINGLDVA LDLYLNEGPE AVWARHALTA KAMRAGVTAM GLSVWAASDS
IASPTTTAVR TPDGVDEKAL RQAARARYGV VFSSGRGETL GKLTRIGHMG PTAQPIYAIA
ALTALGGAMN AAGRKLAIGK GIEAALAVID ADA
