DAPAT_METTH
ID DAPAT_METTH Reviewed; 410 AA.
AC O26158;
DT 01-JUL-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=LL-diaminopimelate aminotransferase {ECO:0000255|HAMAP-Rule:MF_01642, ECO:0000303|PubMed:18371309};
DE Short=DAP-AT {ECO:0000255|HAMAP-Rule:MF_01642, ECO:0000303|PubMed:18371309};
DE Short=DAP-aminotransferase {ECO:0000255|HAMAP-Rule:MF_01642, ECO:0000303|PubMed:18371309};
DE Short=LL-DAP-aminotransferase {ECO:0000255|HAMAP-Rule:MF_01642, ECO:0000303|PubMed:18371309};
DE EC=2.6.1.83 {ECO:0000255|HAMAP-Rule:MF_01642, ECO:0000269|PubMed:18310350, ECO:0000269|PubMed:18371309};
GN Name=dapL {ECO:0000255|HAMAP-Rule:MF_01642}; OrderedLocusNames=MTH_52;
OS Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM
OS 10044 / NBRC 100330 / Delta H) (Methanobacterium thermoautotrophicum).
OC Archaea; Euryarchaeota; Methanomada group; Methanobacteria;
OC Methanobacteriales; Methanobacteriaceae; Methanothermobacter.
OX NCBI_TaxID=187420;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H;
RX PubMed=9371463; DOI=10.1128/jb.179.22.7135-7155.1997;
RA Smith D.R., Doucette-Stamm L.A., Deloughery C., Lee H.-M., Dubois J.,
RA Aldredge T., Bashirzadeh R., Blakely D., Cook R., Gilbert K., Harrison D.,
RA Hoang L., Keagle P., Lumm W., Pothier B., Qiu D., Spadafora R., Vicare R.,
RA Wang Y., Wierzbowski J., Gibson R., Jiwani N., Caruso A., Bush D.,
RA Safer H., Patwell D., Prabhakar S., McDougall S., Shimer G., Goyal A.,
RA Pietrovski S., Church G.M., Daniels C.J., Mao J.-I., Rice P., Noelling J.,
RA Reeve J.N.;
RT "Complete genome sequence of Methanobacterium thermoautotrophicum deltaH:
RT functional analysis and comparative genomics.";
RL J. Bacteriol. 179:7135-7155(1997).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR, AND PATHWAY.
RC STRAIN=ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H;
RX PubMed=18371309; DOI=10.1016/j.febslet.2008.03.021;
RA Graham D.E., Huse H.K.;
RT "Methanogens with pseudomurein use diaminopimelate aminotransferase in
RT lysine biosynthesis.";
RL FEBS Lett. 582:1369-1374(2008).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE
RP SPECIFICITY, AND PATHWAY.
RC STRAIN=ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H;
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. Is also able to catalyze the reverse reaction in
CC vitro, i.e. the transamination of LL-diaminopimelate with 2-
CC oxoglutarate to produce 2-oxo-6-aminopimelate (in equilibrium with
CC tetrahydrodipicolinate) and glutamate. Has maximal aminotransferase
CC activity using 2-oxoglutarate as an amino group acceptor, and cannot
CC use oxaloacetate instead of 2-oxoglutarate, although 2-oxoadipate can
CC substitute with 21% relative activity. Cannot use m-DAP, lysine or
CC ornithine as the amino-group donor, when using 2-oxoglutarate as the
CC amino-group acceptor. {ECO:0000269|PubMed:18310350,
CC ECO:0000269|PubMed:18371309}.
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, ECO:0000269|PubMed:18310350,
CC ECO:0000269|PubMed:18371309};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01642,
CC ECO:0000269|PubMed:18371309};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=82 uM for LL-2,6-diaminopimelate {ECO:0000269|PubMed:18310350};
CC KM=7.8 uM for L-2,3,4,5-tetrahydrodipicolinate
CC {ECO:0000269|PubMed:18310350};
CC KM=2.6 mM for 2-oxoglutarate {ECO:0000269|PubMed:18310350};
CC KM=1.1 mM for glutamate {ECO:0000269|PubMed:18310350};
CC Vmax=6.3 umol/min/mg enzyme for the forward reaction
CC (tetrahydrodipicolinate synthesis) {ECO:0000269|PubMed:18310350};
CC Vmax=0.100 umol/min/mg enzyme for the reverse reaction (LL-DAP
CC synthesis) {ECO:0000269|PubMed:18310350};
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, ECO:0000269|PubMed:18371309}.
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; AE000666; AAB84559.1; -; Genomic_DNA.
DR PIR; E69168; E69168.
DR RefSeq; WP_010875692.1; NC_000916.1.
DR AlphaFoldDB; O26158; -.
DR SMR; O26158; -.
DR STRING; 187420.MTH_52; -.
DR PRIDE; O26158; -.
DR EnsemblBacteria; AAB84559; AAB84559; MTH_52.
DR GeneID; 1470014; -.
DR KEGG; mth:MTH_52; -.
DR PATRIC; fig|187420.15.peg.50; -.
DR HOGENOM; CLU_051433_0_0_2; -.
DR OMA; DFQARGC; -.
DR BRENDA; 2.6.1.83; 3256.
DR SABIO-RK; O26158; -.
DR UniPathway; UPA00034; UER00466.
DR Proteomes; UP000005223; 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; IPR019942; DapL/ALD1.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR PANTHER; PTHR43144; PTHR43144; 1.
DR Pfam; PF00155; Aminotran_1_2; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
DR TIGRFAMs; TIGR03542; DAPAT_plant; 1.
PE 1: Evidence at protein level;
KW Aminotransferase; Pyridoxal phosphate; Reference proteome; Transferase.
FT CHAIN 1..410
FT /note="LL-diaminopimelate aminotransferase"
FT /id="PRO_0000342256"
FT BINDING 15
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 42
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 72
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 108..109
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 109
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 132
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 132
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 187
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 187
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 218
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 246..248
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 257
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 292
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 292
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT BINDING 388
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
FT MOD_RES 249
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01642"
SQ SEQUENCE 410 AA; 46213 MW; A9B03194E73DED5B CRC64;
MVTVNENYLL LKSSYIFSEI NRRVEEFQRK NPDADIIRMG IGDVTRPLPE AVVEAFHRAV
DEMAEEETFR GYGPEQGYPF LREAIAENDY ASRGVDITAD EIFISDGAKC DTGNIQEIFG
LDNVVAVTDP VYPVYVESNV MAGRAGPADD DGRYSGLVYL PCTEENSFIP SLPEERVDLI
YLCYPNNPTG TTLTEKQLAE WVDYARDSGS LILFDAAYEA YIQEDGIPHS IYEVEGAREV
AIEFRSFSKN AGFTGTRCAF TVVPEELEVP DSSGRMHSVR ELWNRRQTTK FNGVSYPVQR
AAEAVYTPEG QREIRESIDY YMENARIIRE SLERAGLRYY GGVNAPYIWI RTPEGMDSWQ
FFDTLLNDAE VVGTPGSGFG PSGEGYFRLT AFNSFRNTVK AMERISELSF
