DAPAT_SYNFM
ID DAPAT_SYNFM Reviewed; 388 AA.
AC A0LEA5;
DT 01-JUL-2008, integrated into UniProtKB/Swiss-Prot.
DT 12-DEC-2006, sequence version 1.
DT 03-AUG-2022, entry version 90.
DE RecName: Full=LL-diaminopimelate aminotransferase {ECO:0000255|HAMAP-Rule:MF_01642, ECO:0000303|PubMed:18310350};
DE Short=DAP-AT {ECO:0000255|HAMAP-Rule:MF_01642, ECO:0000303|PubMed:18310350};
DE Short=DAP-aminotransferase {ECO:0000255|HAMAP-Rule:MF_01642, ECO:0000303|PubMed:18310350};
DE Short=LL-DAP-aminotransferase {ECO:0000255|HAMAP-Rule:MF_01642, ECO:0000303|PubMed:18310350};
DE EC=2.6.1.83 {ECO:0000255|HAMAP-Rule:MF_01642};
GN Name=dapL {ECO:0000255|HAMAP-Rule:MF_01642}; OrderedLocusNames=Sfum_0054;
OS Syntrophobacter fumaroxidans (strain DSM 10017 / MPOB).
OC Bacteria; Proteobacteria; Deltaproteobacteria; Syntrophobacterales;
OC Syntrophobacteraceae; Syntrophobacter.
OX NCBI_TaxID=335543;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 10017 / MPOB;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Hammon N., Israni S., Pitluck S., Goltsman E.G.,
RA Martinez M., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N.,
RA Kim E., Boone D.R., Brockman F., Culley D., Ferry J., Gunsalus R.,
RA McInerney M.J., Morrison M., Plugge C., Rohlin L., Scholten J., Sieber J.,
RA Stams A.J.M., Worm P., Henstra A.M., Richardson P.;
RT "Complete sequence of Syntrophobacter fumaroxidans MPOB.";
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP FUNCTION AS A LL-DAP AMINOTRANSFERASE, SUBSTRATE SPECIFICITY, AND PATHWAY.
RX PubMed=18310350; DOI=10.1128/jb.01381-07;
RA Hudson A.O., Gilvarg C., Leustek T.;
RT "Biochemical and phylogenetic characterization of a novel diaminopimelate
RT biosynthesis pathway in prokaryotes identifies a diverged form of LL-
RT diaminopimelate aminotransferase.";
RL J. Bacteriol. 190:3256-3263(2008).
CC -!- FUNCTION: Involved in the synthesis of meso-diaminopimelate (m-DAP or
CC DL-DAP), required for both lysine and peptidoglycan biosynthesis.
CC Catalyzes the direct conversion of tetrahydrodipicolinate to LL-
CC diaminopimelate. Can also use m-DAP instead of LL-DAP as the amino-
CC group donor. {ECO:0000269|PubMed:18310350}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2S,6S)-2,6-diaminoheptanedioate + 2-oxoglutarate = (S)-
CC 2,3,4,5-tetrahydrodipicolinate + H(+) + H2O + L-glutamate;
CC Xref=Rhea:RHEA:23988, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:16845, ChEBI:CHEBI:29985,
CC ChEBI:CHEBI:57609; EC=2.6.1.83; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01642};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01642};
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate
CC (aminotransferase route): step 1/1. {ECO:0000255|HAMAP-Rule:MF_01642,
CC ECO:0000269|PubMed:18310350}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01642}.
CC -!- SIMILARITY: Belongs to the class-I pyridoxal-phosphate-dependent
CC aminotransferase family. LL-diaminopimelate aminotransferase subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_01642}.
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DR EMBL; CP000478; ABK15757.1; -; Genomic_DNA.
DR RefSeq; WP_011696930.1; NC_008554.1.
DR AlphaFoldDB; A0LEA5; -.
DR SMR; A0LEA5; -.
DR STRING; 335543.Sfum_0054; -.
DR EnsemblBacteria; ABK15757; ABK15757; Sfum_0054.
DR KEGG; sfu:Sfum_0054; -.
DR eggNOG; COG0436; Bacteria.
DR HOGENOM; CLU_017584_4_5_7; -.
DR OMA; DFQARGC; -.
DR OrthoDB; 417859at2; -.
DR BRENDA; 2.6.1.83; 746.
DR UniPathway; UPA00034; UER00466.
DR Proteomes; UP000001784; Chromosome.
DR GO; GO:0010285; F:L,L-diaminopimelate aminotransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:UniProtKB-UniRule.
DR GO; GO:0033362; P:lysine biosynthetic process via diaminopimelate, diaminopimelate-aminotransferase pathway; IEA:UniProtKB-UniRule.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR HAMAP; MF_01642; DapL_aminotrans_1; 1.
DR InterPro; IPR004839; Aminotransferase_I/II.
DR InterPro; IPR019881; DAP-NH2Trfase_DapL_Desulfo.
DR InterPro; IPR019942; DapL/ALD1.
DR InterPro; IPR004838; NHTrfase_class1_PyrdxlP-BS.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR Pfam; PF00155; Aminotran_1_2; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
DR TIGRFAMs; TIGR03540; DapC_direct; 1.
DR PROSITE; PS00105; AA_TRANSFER_CLASS_1; 1.
PE 1: Evidence at protein level;
KW Aminotransferase; Pyridoxal phosphate; Reference proteome; Transferase.
FT CHAIN 1..388
FT /note="LL-diaminopimelate aminotransferase"
FT /id="PRO_0000342255"
FT BINDING 15
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 40
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 69
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 103..104
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 104
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 128
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 128
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 178
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 178
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 209
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 237..239
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 248
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 366
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT MOD_RES 240
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
SQ SEQUENCE 388 AA; 42619 MW; 2A5B75E824CA6421 CRC64;
MAFVKAERLK LLPPYLFQEI DRLKAELTAK GVDVINLGVG DPDLPTPDHI IARLKTAAED
PSTHQYPSYS GMNDFKVSVA GWYKRRFGVE LDPLSEVLTL IGSKEGLAHF PLAVINPGDL
ALVPTPAYPV YHVATMFAGG ESYFMPLVRE NGFLPDLDSI PADVARRAKV MFINYPNNPT
GATAERDFFE KVIAFAREYD VIVCHDAAYT EMAFGGYRPL SFLELPGAGE VGVEFHSLSK
TYNMTGWRLG FAVGNADILA GLGQVKSNID SGAFNAVQWA GITALEGDQG CVVEMQRIYK
ERLDILIEGL KRIGLHPEVP RATFYVWCPT PPGYSSKDFS SLLLREAGIV ATPGSGFGAP
GEGYIRMALT VDKERVREAV ERMRKLSF
