DAPAT_CHLTR
ID DAPAT_CHLTR Reviewed; 394 AA.
AC O84395; A3FKT7;
DT 04-DEC-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 2.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=LL-diaminopimelate aminotransferase {ECO:0000255|HAMAP-Rule:MF_01642, ECO:0000303|PubMed:17093042};
DE Short=DAP-AT {ECO:0000255|HAMAP-Rule:MF_01642, ECO:0000303|PubMed:17093042};
DE Short=DAP-aminotransferase {ECO:0000255|HAMAP-Rule:MF_01642, ECO:0000303|PubMed:17093042};
DE Short=LL-DAP-aminotransferase {ECO:0000255|HAMAP-Rule:MF_01642, ECO:0000303|PubMed:17093042};
DE EC=2.6.1.83 {ECO:0000255|HAMAP-Rule:MF_01642, ECO:0000269|PubMed:17093042};
GN Name=dapL {ECO:0000255|HAMAP-Rule:MF_01642}; Synonyms=aspC;
GN OrderedLocusNames=CT_390;
OS Chlamydia trachomatis (strain D/UW-3/Cx).
OC Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae;
OC Chlamydia/Chlamydophila group; Chlamydia.
OX NCBI_TaxID=272561;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], CATALYTIC ACTIVITY, FUNCTION,
RP BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, DEVELOPMENTAL STAGE, AND SUBSTRATE
RP SPECIFICITY.
RC STRAIN=L2;
RX PubMed=17093042; DOI=10.1073/pnas.0608643103;
RA McCoy A.J., Adams N.E., Hudson A.O., Gilvarg C., Leustek T., Maurelli A.T.;
RT "L,L-diaminopimelate aminotransferase, a trans-kingdom enzyme shared by
RT Chlamydia and plants for synthesis of diaminopimelate/lysine.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:17909-17914(2006).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=D/UW-3/Cx;
RX PubMed=9784136; DOI=10.1126/science.282.5389.754;
RA Stephens R.S., Kalman S., Lammel C.J., Fan J., Marathe R., Aravind L.,
RA Mitchell W.P., Olinger L., Tatusov R.L., Zhao Q., Koonin E.V., Davis R.W.;
RT "Genome sequence of an obligate intracellular pathogen of humans: Chlamydia
RT trachomatis.";
RL Science 282:754-759(1998).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE
RP ANALOG, FUNCTION, COFACTOR, AND SUBUNIT.
RX PubMed=21722650; DOI=10.1016/j.jmb.2011.06.023;
RA Watanabe N., Clay M.D., van Belkum M.J., Fan C., Vederas J.C., James M.N.;
RT "The structure of LL-diaminopimelate aminotransferase from Chlamydia
RT trachomatis: implications for its broad substrate specificity.";
RL J. Mol. Biol. 411:649-660(2011).
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 (PubMed:17093042, PubMed:21722650). Is also able to use
CC meso-diaminopimelate, cystathionine, lysine or ornithine as substrates
CC (PubMed:17093042). {ECO:0000269|PubMed:17093042,
CC ECO:0000269|PubMed:21722650}.
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:17093042};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01642,
CC ECO:0000269|PubMed:17093042, ECO:0000269|PubMed:21722650};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=116 uM for LL-2,6-diaminopimelate (at 30 degrees Celsius and pH
CC 7.6) {ECO:0000269|PubMed:17093042};
CC KM=2.1 mM for 2-oxoglutarate (at 30 degrees Celsius and pH 7.6)
CC {ECO:0000269|PubMed:17093042};
CC KM=19 uM for L-2,3,4,5-tetrahydrodipicolinate (at 30 degrees Celsius
CC and pH 7.6) {ECO:0000269|PubMed:17093042};
CC KM=4.0 mM for glutamic acid (at 30 degrees Celsius and pH 7.6)
CC {ECO:0000269|PubMed:17093042};
CC Vmax=0.58 umol/min/mg enzyme for the forward reaction (at 30 degrees
CC Celsius and pH 7.6) {ECO:0000269|PubMed:17093042};
CC Vmax=0.01 umol/min/mg enzyme for the reverse reaction (at 30 degrees
CC Celsius and pH 7.6) {ECO:0000269|PubMed:17093042};
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 -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01642,
CC ECO:0000269|PubMed:21722650}.
CC -!- DEVELOPMENTAL STAGE: Expressed as early as 8 hours after infection.
CC {ECO:0000269|PubMed:17093042}.
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; EF396248; ABN58777.1; -; Genomic_DNA.
DR EMBL; AE001273; AAC67987.2; -; Genomic_DNA.
DR PIR; D71520; D71520.
DR RefSeq; NP_219900.1; NC_000117.1.
DR RefSeq; WP_009871742.1; NC_000117.1.
DR PDB; 3ASA; X-ray; 2.05 A; A=1-394.
DR PDB; 3ASB; X-ray; 2.70 A; A=1-394.
DR PDBsum; 3ASA; -.
DR PDBsum; 3ASB; -.
DR AlphaFoldDB; O84395; -.
DR SMR; O84395; -.
DR STRING; 813.O172_02125; -.
DR EnsemblBacteria; AAC67987; AAC67987; CT_390.
DR GeneID; 884727; -.
DR KEGG; ctr:CT_390; -.
DR PATRIC; fig|272561.5.peg.420; -.
DR HOGENOM; CLU_051433_0_0_0; -.
DR InParanoid; O84395; -.
DR OMA; DFQARGC; -.
DR BRENDA; 2.6.1.83; 1315.
DR SABIO-RK; O84395; -.
DR UniPathway; UPA00034; UER00466.
DR EvolutionaryTrace; O84395; -.
DR Proteomes; UP000000431; Chromosome.
DR GO; GO:0010285; F:L,L-diaminopimelate aminotransferase activity; IDA:UniProtKB.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IDA:UniProtKB.
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; 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 PANTHER; PTHR43144; PTHR43144; 1.
DR Pfam; PF00155; Aminotran_1_2; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
DR TIGRFAMs; TIGR03542; DAPAT_plant; 1.
DR PROSITE; PS00105; AA_TRANSFER_CLASS_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aminotransferase; Pyridoxal phosphate; Reference proteome;
KW Transferase.
FT CHAIN 1..394
FT /note="LL-diaminopimelate aminotransferase"
FT /id="PRO_0000312004"
FT BINDING 14
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q93ZN9,
FT ECO:0000305|PubMed:21722650"
FT BINDING 41
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q93ZN9"
FT BINDING 71
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:Q93ZN9"
FT BINDING 104..105
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:21722650"
FT BINDING 105
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q93ZN9"
FT BINDING 128
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000305|PubMed:21722650"
FT BINDING 128
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q93ZN9,
FT ECO:0000305|PubMed:21722650"
FT BINDING 174
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:21722650"
FT BINDING 174
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q93ZN9,
FT ECO:0000305|PubMed:21722650"
FT BINDING 205
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:21722650"
FT BINDING 233..235
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:21722650"
FT BINDING 244
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:Q93ZN9"
FT BINDING 275
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:Q93ZN9,
FT ECO:0000305|PubMed:21722650"
FT BINDING 275
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q93ZN9"
FT BINDING 369
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q93ZN9"
FT MOD_RES 236
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000269|PubMed:21722650"
FT CONFLICT 92
FT /note="F -> C (in Ref. 1; ABN58777)"
FT /evidence="ECO:0000305"
FT CONFLICT 106
FT /note="V -> A (in Ref. 1; ABN58777)"
FT /evidence="ECO:0000305"
FT HELIX 5..8
FT /evidence="ECO:0007829|PDB:3ASA"
FT HELIX 15..29
FT /evidence="ECO:0007829|PDB:3ASA"
FT HELIX 49..62
FT /evidence="ECO:0007829|PDB:3ASA"
FT STRAND 64..66
FT /evidence="ECO:0007829|PDB:3ASA"
FT HELIX 78..86
FT /evidence="ECO:0007829|PDB:3ASA"
FT HELIX 95..97
FT /evidence="ECO:0007829|PDB:3ASA"
FT STRAND 98..102
FT /evidence="ECO:0007829|PDB:3ASA"
FT HELIX 104..115
FT /evidence="ECO:0007829|PDB:3ASA"
FT STRAND 120..126
FT /evidence="ECO:0007829|PDB:3ASA"
FT HELIX 129..137
FT /evidence="ECO:0007829|PDB:3ASA"
FT STRAND 141..147
FT /evidence="ECO:0007829|PDB:3ASA"
FT HELIX 150..152
FT /evidence="ECO:0007829|PDB:3ASA"
FT STRAND 165..172
FT /evidence="ECO:0007829|PDB:3ASA"
FT TURN 174..176
FT /evidence="ECO:0007829|PDB:3ASA"
FT HELIX 182..194
FT /evidence="ECO:0007829|PDB:3ASA"
FT STRAND 198..202
FT /evidence="ECO:0007829|PDB:3ASA"
FT HELIX 206..208
FT /evidence="ECO:0007829|PDB:3ASA"
FT HELIX 218..220
FT /evidence="ECO:0007829|PDB:3ASA"
FT HELIX 224..226
FT /evidence="ECO:0007829|PDB:3ASA"
FT STRAND 228..233
FT /evidence="ECO:0007829|PDB:3ASA"
FT HELIX 236..238
FT /evidence="ECO:0007829|PDB:3ASA"
FT STRAND 246..249
FT /evidence="ECO:0007829|PDB:3ASA"
FT HELIX 262..273
FT /evidence="ECO:0007829|PDB:3ASA"
FT HELIX 279..291
FT /evidence="ECO:0007829|PDB:3ASA"
FT TURN 292..294
FT /evidence="ECO:0007829|PDB:3ASA"
FT HELIX 296..314
FT /evidence="ECO:0007829|PDB:3ASA"
FT STRAND 318..321
FT /evidence="ECO:0007829|PDB:3ASA"
FT STRAND 323..331
FT /evidence="ECO:0007829|PDB:3ASA"
FT TURN 339..341
FT /evidence="ECO:0007829|PDB:3ASA"
FT HELIX 342..350
FT /evidence="ECO:0007829|PDB:3ASA"
FT STRAND 351..353
FT /evidence="ECO:0007829|PDB:3ASA"
FT HELIX 357..360
FT /evidence="ECO:0007829|PDB:3ASA"
FT HELIX 362..364
FT /evidence="ECO:0007829|PDB:3ASA"
FT STRAND 368..371
FT /evidence="ECO:0007829|PDB:3ASA"
FT HELIX 376..387
FT /evidence="ECO:0007829|PDB:3ASA"
SQ SEQUENCE 394 AA; 43841 MW; 98437E24E6D55AAE CRC64;
MKRNPHFVSL TKNYLFADLQ KRVAQFRLEN PQHTVINLSI GDTTQPLNAS VAEAFASSIA
RLSSPTTCRG YGPDFGLPAL RQKLSEDFYR GFVDAKEIFI SDGAKVDLFR LLSFFGPNQT
VAIQDPSYPA YLDIARLTGA KEIIALPCLQ ENAFFPEFPE DTHIDILCLC SPNNPTGTVL
NKDQLRAIVH YAIEHEILIL FDAAYSTFIS DPSLPKSIFE IPDARFCAIE INSFSKPLGF
AGIRLGWTVI PQELTYADGH FVIQDWERFL STTFNGASIP AQEAGVAGLS ILPQLEAIHY
YRENSDLLRK ALLATGFEVF GGEHAPYLWV KPTQANISDR DLFDFFLREY HIAITPGIGF
GRSGSGFVRF SSLGKREDIL AACERLQMAP ALQS
