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Protein

D-3-phosphoglycerate dehydrogenase

Gene

serA

Organism
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

3-phospho-D-glycerate + NAD+ = 3-phosphonooxypyruvate + NADH.
2-hydroxyglutarate + NAD+ = 2-oxoglutarate + NADH.

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

GO - Biological processi

  • growth Source: MTBBASE
  • L-serine biosynthetic process Source: MTBBASE
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Amino-acid biosynthesis, Serine biosynthesis

Keywords - Ligandi

NAD

Enzyme and pathway databases

BioCyciMTBH37RV:G185E-7253-MONOMER.
UniPathwayiUPA00135; UER00196.

Names & Taxonomyi

Protein namesi
Recommended name:
D-3-phosphoglycerate dehydrogenase (EC:1.1.1.95)
Short name:
PGDH
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
Complete GO annotation...

PTM / Processingi

Molecule processing

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

Proteomic databases

PaxDbiP9WNX3.

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

Contains 1 ACT domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4108JQ1. Bacteria.
COG0111. LUCA.
KOiK00058.
OMAiEWKRSKF.
PhylomeDBiP9WNX3.

Family and domain databases

Gene3Di3.30.1330.90. 1 hit.
3.40.50.720. 2 hits.
InterProiIPR002912. ACT_dom.
IPR029009. ASB_dom.
IPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR029753. D-isomer_DH_CS.
IPR029752. D-isomer_DH_CS1.
IPR006140. D-isomer_DH_NAD-bd.
IPR016040. NAD(P)-bd_dom.
IPR006236. PGDH.
[Graphical view]
PfamiPF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
PF01842. ACT. 1 hit.
[Graphical view]
SUPFAMiSSF143548. SSF143548. 1 hit.
SSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01327. PGDH. 1 hit.
PROSITEiPS51671. 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.
[Graphical view]

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.

Cross-referencesi

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.

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...

Protein-protein interaction databases

IntActiP9WNX3. 1 interactor.
STRINGi83332.Rv2996c.

Proteomic databases

PaxDbiP9WNX3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCCP45801; CCP45801; Rv2996c.
GeneIDi887154.
KEGGimtu:Rv2996c.

Organism-specific databases

TubercuListiRv2996c.

Phylogenomic databases

eggNOGiENOG4108JQ1. Bacteria.
COG0111. LUCA.
KOiK00058.
OMAiEWKRSKF.
PhylomeDBiP9WNX3.

Enzyme and pathway databases

UniPathwayiUPA00135; UER00196.
BioCyciMTBH37RV:G185E-7253-MONOMER.

Family and domain databases

Gene3Di3.30.1330.90. 1 hit.
3.40.50.720. 2 hits.
InterProiIPR002912. ACT_dom.
IPR029009. ASB_dom.
IPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR029753. D-isomer_DH_CS.
IPR029752. D-isomer_DH_CS1.
IPR006140. D-isomer_DH_NAD-bd.
IPR016040. NAD(P)-bd_dom.
IPR006236. PGDH.
[Graphical view]
PfamiPF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
PF01842. ACT. 1 hit.
[Graphical view]
SUPFAMiSSF143548. SSF143548. 1 hit.
SSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01327. PGDH. 1 hit.
PROSITEiPS51671. 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.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSERA_MYCTU
AccessioniPrimary (citable) accession number: P9WNX3
Secondary accession number(s): L0TBH1, O53243, P0A544
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 16, 2014
Last sequence update: April 16, 2014
Last modified: November 30, 2016
This is version 21 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Was identified as a high-confidence drug target.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh
    Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.