SERA_MYCTU
ID SERA_MYCTU Reviewed; 528 AA.
AC P9WNX3; L0TBH1; O53243; P0A544;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 46.
DE RecName: Full=D-3-phosphoglycerate dehydrogenase;
DE Short=PGDH;
DE EC=1.1.1.95 {ECO:0000250|UniProtKB:P0A9T0};
DE AltName: Full=2-oxoglutarate reductase {ECO:0000250|UniProtKB:P0A9T0};
DE EC=1.1.1.399 {ECO:0000250|UniProtKB:P0A9T0};
GN Name=serA; OrderedLocusNames=Rv2996c; ORFNames=MTV012.10;
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 IDENTIFICATION AS A DRUG TARGET [LARGE SCALE ANALYSIS].
RX PubMed=19099550; DOI=10.1186/1752-0509-2-109;
RA Raman K., Yeturu K., Chandra N.;
RT "targetTB: a target identification pipeline for Mycobacterium tuberculosis
RT through an interactome, reactome and genome-scale structural analysis.";
RL BMC Syst. Biol. 2:109-109(2008).
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).
CC -!- FUNCTION: Catalyzes the reversible oxidation of 3-phospho-D-glycerate
CC to 3-phosphonooxypyruvate, the first step of the phosphorylated L-
CC serine biosynthesis pathway. Also catalyzes the reversible oxidation of
CC 2-hydroxyglutarate to 2-oxoglutarate. {ECO:0000250|UniProtKB:P0A9T0}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + H(+)
CC + NADH; Xref=Rhea:RHEA:12641, ChEBI:CHEBI:15378, ChEBI:CHEBI:18110,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57945, ChEBI:CHEBI:58272; EC=1.1.1.95;
CC Evidence={ECO:0000250|UniProtKB:P0A9T0};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + H(+) +
CC NADH; Xref=Rhea:RHEA:49612, ChEBI:CHEBI:15378, ChEBI:CHEBI:15801,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945;
CC EC=1.1.1.399; Evidence={ECO:0000250|UniProtKB:P0A9T0};
CC -!- PATHWAY: Amino-acid biosynthesis; L-serine biosynthesis; L-serine from
CC 3-phospho-D-glycerate: step 1/3.
CC -!- MISCELLANEOUS: Was identified as a high-confidence drug target.
CC -!- SIMILARITY: Belongs to the D-isomer specific 2-hydroxyacid
CC dehydrogenase family. {ECO:0000305}.
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DR EMBL; AL123456; CCP45801.1; -; Genomic_DNA.
DR PIR; G70854; G70854.
DR RefSeq; WP_003899578.1; NZ_NVQJ01000041.1.
DR RefSeq; YP_177916.1; NC_000962.3.
DR PDB; 1YGY; X-ray; 2.30 A; A/B=2-528.
DR PDB; 3DC2; X-ray; 2.70 A; A/B=2-528.
DR PDB; 3DDN; X-ray; 2.40 A; A/B=2-528.
DR PDBsum; 1YGY; -.
DR PDBsum; 3DC2; -.
DR PDBsum; 3DDN; -.
DR AlphaFoldDB; P9WNX3; -.
DR SMR; P9WNX3; -.
DR IntAct; P9WNX3; 1.
DR STRING; 83332.Rv2996c; -.
DR DrugBank; DB01694; D-tartaric acid.
DR PaxDb; P9WNX3; -.
DR DNASU; 887154; -.
DR GeneID; 45426986; -.
DR GeneID; 887154; -.
DR KEGG; mtu:Rv2996c; -.
DR TubercuList; Rv2996c; -.
DR eggNOG; COG0111; Bacteria.
DR OMA; NIAGMQV; -.
DR PhylomeDB; P9WNX3; -.
DR BRENDA; 1.1.1.95; 3445.
DR UniPathway; UPA00135; UER00196.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0009274; C:peptidoglycan-based cell wall; HDA:MTBBASE.
DR GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0004617; F:phosphoglycerate dehydrogenase activity; IDA:MTBBASE.
DR GO; GO:0006564; P:L-serine biosynthetic process; IDA:MTBBASE.
DR Gene3D; 3.30.1330.90; -; 1.
DR InterPro; IPR045865; ACT-like_dom_sf.
DR InterPro; IPR002912; ACT_dom.
DR InterPro; IPR029009; ASB_dom_sf.
DR InterPro; IPR006139; D-isomer_2_OHA_DH_cat_dom.
DR InterPro; IPR029753; D-isomer_DH_CS.
DR InterPro; IPR029752; D-isomer_DH_CS1.
DR InterPro; IPR006140; D-isomer_DH_NAD-bd.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR006236; PGDH.
DR InterPro; IPR045626; PGDH_ASB_dom.
DR Pfam; PF00389; 2-Hacid_dh; 1.
DR Pfam; PF02826; 2-Hacid_dh_C; 1.
DR Pfam; PF01842; ACT; 1.
DR Pfam; PF19304; PGDH_inter; 1.
DR SUPFAM; SSF143548; SSF143548; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR SUPFAM; SSF55021; SSF55021; 1.
DR TIGRFAMs; TIGR01327; PGDH; 1.
DR PROSITE; PS51671; ACT; 1.
DR PROSITE; PS00065; D_2_HYDROXYACID_DH_1; 1.
DR PROSITE; PS00670; D_2_HYDROXYACID_DH_2; 1.
DR PROSITE; PS00671; D_2_HYDROXYACID_DH_3; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; NAD; Oxidoreductase;
KW Reference proteome; Serine biosynthesis.
FT CHAIN 1..528
FT /note="D-3-phosphoglycerate dehydrogenase"
FT /id="PRO_0000076005"
FT DOMAIN 455..527
FT /note="ACT"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01007"
FT ACT_SITE 232
FT /evidence="ECO:0000250"
FT ACT_SITE 261
FT /evidence="ECO:0000250"
FT ACT_SITE 279
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 151..152
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 171
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 230..232
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 256
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 279..282
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT STRAND 5..8
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 14..17
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 22..28
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 34..40
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 41..43
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 45..49
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 51..53
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 57..61
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 68..74
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 81..86
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 90..92
FT /evidence="ECO:0007829|PDB:1YGY"
FT TURN 95..98
FT /evidence="ECO:0007829|PDB:3DDN"
FT HELIX 99..114
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 117..125
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 131..133
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 143..147
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 151..161
FT /evidence="ECO:0007829|PDB:1YGY"
FT TURN 162..164
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 166..170
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 176..182
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 189..195
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 197..201
FT /evidence="ECO:0007829|PDB:1YGY"
FT TURN 207..211
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 215..218
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 226..229
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 238..246
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 248..250
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 252..257
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 259..262
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 267..270
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 274..276
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 285..303
FT /evidence="ECO:0007829|PDB:1YGY"
FT TURN 321..325
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 326..339
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 341..343
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 346..354
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 355..358
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 362..372
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 374..376
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 386..393
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 396..403
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 406..417
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 423..431
FT /evidence="ECO:0007829|PDB:1YGY"
FT TURN 432..435
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 436..442
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 445..451
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 453..461
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 466..476
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 481..488
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 490..493
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 495..503
FT /evidence="ECO:0007829|PDB:1YGY"
FT HELIX 507..517
FT /evidence="ECO:0007829|PDB:1YGY"
FT STRAND 519..526
FT /evidence="ECO:0007829|PDB:1YGY"
SQ SEQUENCE 528 AA; 54554 MW; 3B5696AAFD82A901 CRC64;
MSLPVVLIAD KLAPSTVAAL GDQVEVRWVD GPDRDKLLAA VPEADALLVR SATTVDAEVL
AAAPKLKIVA RAGVGLDNVD VDAATARGVL VVNAPTSNIH SAAEHALALL LAASRQIPAA
DASLREHTWK RSSFSGTEIF GKTVGVVGLG RIGQLVAQRI AAFGAYVVAY DPYVSPARAA
QLGIELLSLD DLLARADFIS VHLPKTPETA GLIDKEALAK TKPGVIIVNA ARGGLVDEAA
LADAITGGHV RAAGLDVFAT EPCTDSPLFE LAQVVVTPHL GASTAEAQDR AGTDVAESVR
LALAGEFVPD AVNVGGGVVN EEVAPWLDLV RKLGVLAGVL SDELPVSLSV QVRGELAAEE
VEVLRLSALR GLFSAVIEDA VTFVNAPALA AERGVTAEIC KASESPNHRS VVDVRAVGAD
GSVVTVSGTL YGPQLSQKIV QINGRHFDLR AQGINLIIHY VDRPGALGKI GTLLGTAGVN
IQAAQLSEDA EGPGATILLR LDQDVPDDVR TAIAAAVDAY KLEVVDLS
