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Protein

D-3-phosphoglycerate dehydrogenase

Gene

serA

Organism
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L-serine biosynthesis pathway. Also catalyzes the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate.By similarity

Miscellaneous

Was identified as a high-confidence drug target.

Catalytic activityi

3-phospho-D-glycerate + NAD+ = 3-phosphonooxypyruvate + NADH.By similarity
(R)-2-hydroxyglutarate + NAD+ = 2-oxoglutarate + NADH.By similarity

Pathwayi: L-serine biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes L-serine from 3-phospho-D-glycerate.
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. D-3-phosphoglycerate dehydrogenase (LH57_16350), D-3-phosphoglycerate dehydrogenase (serA)
  2. Phosphoserine aminotransferase (serC), Phosphoserine aminotransferase (serC)
  3. Phosphoserine phosphatase SerB2 (serB2)
This subpathway is part of the pathway L-serine biosynthesis, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-serine from 3-phospho-D-glycerate, the pathway L-serine biosynthesis and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei171NADBy similarity1
Active sitei232By similarity1
Binding sitei256NADBy similarity1
Active sitei261By similarity1
Active sitei279Proton donorBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi151 – 152NADBy similarity2
Nucleotide bindingi230 – 232NADBy similarity3
Nucleotide bindingi279 – 282NADBy similarity4

GO - Molecular functioni

  • NAD binding Source: InterPro
  • phosphoglycerate dehydrogenase activity Source: MTBBASE

GO - Biological processi

  • growth Source: MTBBASE
  • L-serine biosynthetic process Source: MTBBASE

Keywordsi

Molecular functionOxidoreductase
Biological processAmino-acid biosynthesis, Serine biosynthesis
LigandNAD

Enzyme and pathway databases

UniPathwayiUPA00135; UER00196

Names & Taxonomyi

Protein namesi
Recommended name:
D-3-phosphoglycerate dehydrogenase (EC:1.1.1.95By similarity)
Short name:
PGDH
Alternative name(s):
2-oxoglutarate reductaseBy similarity (EC:1.1.1.399By similarity)
Gene namesi
Name:serA
Ordered Locus Names:Rv2996c
ORF Names:MTV012.10
OrganismiMycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Taxonomic identifieri83332 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
Proteomesi
  • UP000001584 Componenti: Chromosome

Organism-specific databases

TubercuListiRv2996c

Subcellular locationi

GO - Cellular componenti

  • cell wall Source: MTBBASE
  • plasma membrane Source: MTBBASE

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000760051 – 528D-3-phosphoglycerate dehydrogenaseAdd BLAST528

Proteomic databases

PaxDbiP9WNX3
PRIDEiP9WNX3

Interactioni

Protein-protein interaction databases

IntActiP9WNX3, 1 interactor
STRINGi83332.Rv2996c

Structurei

Secondary structure

1528
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 8Combined sources4
Helixi14 – 17Combined sources4
Beta strandi22 – 28Combined sources7
Helixi34 – 40Combined sources7
Helixi41 – 43Combined sources3
Beta strandi45 – 49Combined sources5
Beta strandi51 – 53Combined sources3
Helixi57 – 61Combined sources5
Beta strandi68 – 74Combined sources7
Helixi81 – 86Combined sources6
Beta strandi90 – 92Combined sources3
Turni95 – 98Combined sources4
Helixi99 – 114Combined sources16
Helixi117 – 125Combined sources9
Helixi131 – 133Combined sources3
Beta strandi143 – 147Combined sources5
Helixi151 – 161Combined sources11
Turni162 – 164Combined sources3
Beta strandi166 – 170Combined sources5
Helixi176 – 182Combined sources7
Helixi189 – 195Combined sources7
Beta strandi197 – 201Combined sources5
Turni207 – 211Combined sources5
Helixi215 – 218Combined sources4
Beta strandi226 – 229Combined sources4
Helixi238 – 246Combined sources9
Beta strandi248 – 250Combined sources3
Beta strandi252 – 257Combined sources6
Beta strandi259 – 262Combined sources4
Helixi267 – 270Combined sources4
Beta strandi274 – 276Combined sources3
Helixi285 – 303Combined sources19
Turni321 – 325Combined sources5
Helixi326 – 339Combined sources14
Beta strandi341 – 343Combined sources3
Beta strandi346 – 354Combined sources9
Helixi355 – 358Combined sources4
Helixi362 – 372Combined sources11
Helixi374 – 376Combined sources3
Helixi386 – 393Combined sources8
Beta strandi396 – 403Combined sources8
Beta strandi406 – 417Combined sources12
Beta strandi423 – 431Combined sources9
Turni432 – 435Combined sources4
Beta strandi436 – 442Combined sources7
Beta strandi445 – 451Combined sources7
Beta strandi453 – 461Combined sources9
Helixi466 – 476Combined sources11
Beta strandi481 – 488Combined sources8
Beta strandi490 – 493Combined sources4
Beta strandi495 – 503Combined sources9
Helixi507 – 517Combined sources11
Beta strandi519 – 526Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1YGYX-ray2.30A/B2-528[»]
3DC2X-ray2.70A/B2-528[»]
3DDNX-ray2.40A/B2-528[»]
ProteinModelPortaliP9WNX3
SMRiP9WNX3
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini455 – 527ACTPROSITE-ProRule annotationAdd BLAST73

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4108JQ1 Bacteria
COG0111 LUCA
KOiK00058
OMAiNIAGMQV
PhylomeDBiP9WNX3

Family and domain databases

Gene3Di3.30.1330.90, 1 hit
InterProiView protein in InterPro
IPR002912 ACT_dom
IPR029009 ASB_dom_sf
IPR006139 D-isomer_2_OHA_DH_cat_dom
IPR029753 D-isomer_DH_CS
IPR029752 D-isomer_DH_CS1
IPR006140 D-isomer_DH_NAD-bd
IPR036291 NAD(P)-bd_dom_sf
IPR006236 PGDH
PfamiView protein in Pfam
PF00389 2-Hacid_dh, 1 hit
PF02826 2-Hacid_dh_C, 1 hit
PF01842 ACT, 1 hit
SUPFAMiSSF143548 SSF143548, 1 hit
SSF51735 SSF51735, 1 hit
TIGRFAMsiTIGR01327 PGDH, 1 hit
PROSITEiView protein in PROSITE
PS51671 ACT, 1 hit
PS00065 D_2_HYDROXYACID_DH_1, 1 hit
PS00670 D_2_HYDROXYACID_DH_2, 1 hit
PS00671 D_2_HYDROXYACID_DH_3, 1 hit

Sequencei

Sequence statusi: Complete.

P9WNX3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLPVVLIAD KLAPSTVAAL GDQVEVRWVD GPDRDKLLAA VPEADALLVR
60 70 80 90 100
SATTVDAEVL AAAPKLKIVA RAGVGLDNVD VDAATARGVL VVNAPTSNIH
110 120 130 140 150
SAAEHALALL LAASRQIPAA DASLREHTWK RSSFSGTEIF GKTVGVVGLG
160 170 180 190 200
RIGQLVAQRI AAFGAYVVAY DPYVSPARAA QLGIELLSLD DLLARADFIS
210 220 230 240 250
VHLPKTPETA GLIDKEALAK TKPGVIIVNA ARGGLVDEAA LADAITGGHV
260 270 280 290 300
RAAGLDVFAT EPCTDSPLFE LAQVVVTPHL GASTAEAQDR AGTDVAESVR
310 320 330 340 350
LALAGEFVPD AVNVGGGVVN EEVAPWLDLV RKLGVLAGVL SDELPVSLSV
360 370 380 390 400
QVRGELAAEE VEVLRLSALR GLFSAVIEDA VTFVNAPALA AERGVTAEIC
410 420 430 440 450
KASESPNHRS VVDVRAVGAD GSVVTVSGTL YGPQLSQKIV QINGRHFDLR
460 470 480 490 500
AQGINLIIHY VDRPGALGKI GTLLGTAGVN IQAAQLSEDA EGPGATILLR
510 520
LDQDVPDDVR TAIAAAVDAY KLEVVDLS
Length:528
Mass (Da):54,554
Last modified:April 16, 2014 - v1
Checksum:i3B5696AAFD82A901
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL123456 Genomic DNA Translation: CCP45801.1
PIRiG70854
RefSeqiWP_003899578.1, NZ_KK339370.1
YP_177916.1, NC_000962.3

Genome annotation databases

EnsemblBacteriaiCCP45801; CCP45801; Rv2996c
GeneIDi887154
KEGGimtu:Rv2996c

Similar proteinsi

Entry informationi

Entry nameiSERA_MYCTU
AccessioniPrimary (citable) accession number: P9WNX3
Secondary accession number(s): L0TBH1, O53243, P0A544
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 16, 2014
Last sequence update: April 16, 2014
Last modified: May 23, 2018
This is version 29 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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