DAPC_MYCTU
ID DAPC_MYCTU Reviewed; 397 AA.
AC P9WPZ5; L0T542; O53870; Q7D954;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 39.
DE RecName: Full=Probable N-succinyldiaminopimelate aminotransferase DapC;
DE AltName: Full=DAP-AT;
DE EC=2.6.1.17;
GN Name=dapC; OrderedLocusNames=Rv0858c;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP SUBUNIT.
RX PubMed=16880560; DOI=10.1107/s1744309106026753;
RA Weyand S., Kefala G., Weiss M.S.;
RT "Cloning, expression, purification, crystallization and preliminary X-ray
RT diffraction analysis of DapC (Rv0858c) from Mycobacterium tuberculosis.";
RL Acta Crystallogr. F 62:794-797(2006).
RN [3]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 2-397, FUNCTION, AND SUBUNIT.
RX PubMed=17292400; DOI=10.1016/j.jmb.2007.01.023;
RA Weyand S., Kefala G., Weiss M.S.;
RT "The three-dimensional structure of N-succinyldiaminopimelate
RT aminotransferase from Mycobacterium tuberculosis.";
RL J. Mol. Biol. 367:825-838(2007).
CC -!- FUNCTION: Involved in the lysine biosynthetic pathways. It catalyzes
CC the transfer of an amino group from L-glutamate to N-succinyl-2-l-
CC amino-6-oxoheptanedioate (N-succinyl-2-l-amino-6-ketopimelate) in a
CC PLP-dependent reaction, yielding as products N-succinyl-l-2,6-
CC diaminoheptanedioate (N-succinyl-diaminopimelate) and 2-oxoglutarate
CC (Probable). {ECO:0000305|PubMed:17292400}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-oxoglutarate + N-succinyl-(2S,6S)-2,6-diaminoheptanedioate =
CC (S)-2-succinylamino-6-oxoheptanedioate + L-glutamate;
CC Xref=Rhea:RHEA:11960, ChEBI:CHEBI:15685, ChEBI:CHEBI:16810,
CC ChEBI:CHEBI:29985, ChEBI:CHEBI:58087; EC=2.6.1.17;
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Note=Binds 1 pyridoxal phosphate per subunit.;
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate
CC (succinylase route): step 2/3.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16880560,
CC ECO:0000269|PubMed:17292400}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the class-III pyridoxal-phosphate-dependent
CC aminotransferase family. {ECO:0000305}.
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DR EMBL; AL123456; CCP43606.1; -; Genomic_DNA.
DR PIR; B70815; B70815.
DR RefSeq; NP_215373.1; NC_000962.3.
DR RefSeq; WP_003404420.1; NZ_NVQJ01000040.1.
DR PDB; 2O0R; X-ray; 2.00 A; A/B=2-397.
DR PDBsum; 2O0R; -.
DR AlphaFoldDB; P9WPZ5; -.
DR SMR; P9WPZ5; -.
DR STRING; 83332.Rv0858c; -.
DR PaxDb; P9WPZ5; -.
DR DNASU; 885784; -.
DR GeneID; 45424824; -.
DR GeneID; 885784; -.
DR KEGG; mtu:Rv0858c; -.
DR TubercuList; Rv0858c; -.
DR eggNOG; COG0436; Bacteria.
DR OMA; SVAMTGW; -.
DR PhylomeDB; P9WPZ5; -.
DR BRENDA; 2.6.1.17; 3445.
DR UniPathway; UPA00034; UER00020.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0009274; C:peptidoglycan-based cell wall; HDA:MTBBASE.
DR GO; GO:0016212; F:kynurenine-oxoglutarate transaminase activity; IBA:GO_Central.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
DR GO; GO:0009016; F:succinyldiaminopimelate transaminase activity; IEA:UniProtKB-EC.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR InterPro; IPR004839; Aminotransferase_I/II.
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.
PE 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; Aminotransferase; Cytoplasm;
KW Lysine biosynthesis; Pyridoxal phosphate; Reference proteome; Transferase.
FT CHAIN 1..397
FT /note="Probable N-succinyldiaminopimelate aminotransferase
FT DapC"
FT /id="PRO_0000414591"
FT BINDING 109..110
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 218..222
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT MOD_RES 232
FT /note="N6-(pyridoxal phosphate)lysine"
FT HELIX 4..9
FT /evidence="ECO:0007829|PDB:2O0R"
FT HELIX 13..22
FT /evidence="ECO:0007829|PDB:2O0R"
FT TURN 23..25
FT /evidence="ECO:0007829|PDB:2O0R"
FT STRAND 27..30
FT /evidence="ECO:0007829|PDB:2O0R"
FT HELIX 40..51
FT /evidence="ECO:0007829|PDB:2O0R"
FT HELIX 64..78
FT /evidence="ECO:0007829|PDB:2O0R"
FT TURN 84..86
FT /evidence="ECO:0007829|PDB:2O0R"
FT STRAND 87..92
FT /evidence="ECO:0007829|PDB:2O0R"
FT HELIX 93..105
FT /evidence="ECO:0007829|PDB:2O0R"
FT STRAND 111..117
FT /evidence="ECO:0007829|PDB:2O0R"
FT HELIX 122..128
FT /evidence="ECO:0007829|PDB:2O0R"
FT STRAND 132..137
FT /evidence="ECO:0007829|PDB:2O0R"
FT STRAND 139..141
FT /evidence="ECO:0007829|PDB:2O0R"
FT STRAND 144..146
FT /evidence="ECO:0007829|PDB:2O0R"
FT HELIX 149..155
FT /evidence="ECO:0007829|PDB:2O0R"
FT STRAND 160..168
FT /evidence="ECO:0007829|PDB:2O0R"
FT TURN 170..172
FT /evidence="ECO:0007829|PDB:2O0R"
FT HELIX 178..190
FT /evidence="ECO:0007829|PDB:2O0R"
FT STRAND 194..198
FT /evidence="ECO:0007829|PDB:2O0R"
FT TURN 200..203
FT /evidence="ECO:0007829|PDB:2O0R"
FT HELIX 214..216
FT /evidence="ECO:0007829|PDB:2O0R"
FT TURN 218..220
FT /evidence="ECO:0007829|PDB:2O0R"
FT HELIX 221..223
FT /evidence="ECO:0007829|PDB:2O0R"
FT STRAND 224..229
FT /evidence="ECO:0007829|PDB:2O0R"
FT TURN 237..239
FT /evidence="ECO:0007829|PDB:2O0R"
FT STRAND 241..245
FT /evidence="ECO:0007829|PDB:2O0R"
FT HELIX 248..261
FT /evidence="ECO:0007829|PDB:2O0R"
FT HELIX 269..279
FT /evidence="ECO:0007829|PDB:2O0R"
FT HELIX 281..305
FT /evidence="ECO:0007829|PDB:2O0R"
FT STRAND 314..321
FT /evidence="ECO:0007829|PDB:2O0R"
FT HELIX 323..325
FT /evidence="ECO:0007829|PDB:2O0R"
FT HELIX 330..341
FT /evidence="ECO:0007829|PDB:2O0R"
FT STRAND 342..344
FT /evidence="ECO:0007829|PDB:2O0R"
FT HELIX 348..351
FT /evidence="ECO:0007829|PDB:2O0R"
FT HELIX 366..368
FT /evidence="ECO:0007829|PDB:2O0R"
FT STRAND 370..373
FT /evidence="ECO:0007829|PDB:2O0R"
FT HELIX 378..388
FT /evidence="ECO:0007829|PDB:2O0R"
FT HELIX 389..392
FT /evidence="ECO:0007829|PDB:2O0R"
SQ SEQUENCE 397 AA; 42209 MW; 2667A0F603D1C4F5 CRC64;
MTVSRLRPYA TTVFAEMSAL ATRIGAVNLG QGFPDEDGPP KMLQAAQDAI AGGVNQYPPG
PGSAPLRRAI AAQRRRHFGV DYDPETEVLV TVGATEAIAA AVLGLVEPGS EVLLIEPFYD
SYSPVVAMAG AHRVTVPLVP DGRGFALDAD ALRRAVTPRT RALIINSPHN PTGAVLSATE
LAAIAEIAVA ANLVVITDEV YEHLVFDHAR HLPLAGFDGM AERTITISSA AKMFNCTGWK
IGWACGPAEL IAGVRAAKQY LSYVGGAPFQ PAVALALDTE DAWVAALRNS LRARRDRLAA
GLTEIGFAVH DSYGTYFLCA DPRPLGYDDS TEFCAALPEK VGVAAIPMSA FCDPAAGQAS
QQADVWNHLV RFTFCKRDDT LDEAIRRLSV LAERPAT
