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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. no protein annotated in this organism
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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei171 – 1711NADBy similarity
Active sitei232 – 2321By similarity
Binding sitei256 – 2561NADBy similarity
Active sitei261 – 2611By similarity
Active sitei279 – 2791Proton donorBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi151 – 1522NADBy similarity
Nucleotide bindingi230 – 2323NADBy similarity
Nucleotide bindingi279 – 2824NADBy similarity

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

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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 528528D-3-phosphoglycerate dehydrogenasePRO_0000076005Add
BLAST

Proteomic databases

PaxDbiP9WNX3.

Interactioni

Protein-protein interaction databases

STRINGi83332.Rv2996c.

Structurei

Secondary structure

1
528
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 84Combined sources
Helixi14 – 174Combined sources
Beta strandi22 – 287Combined sources
Helixi34 – 407Combined sources
Helixi41 – 433Combined sources
Beta strandi45 – 495Combined sources
Beta strandi51 – 533Combined sources
Helixi57 – 615Combined sources
Beta strandi68 – 747Combined sources
Helixi81 – 866Combined sources
Beta strandi90 – 923Combined sources
Turni95 – 984Combined sources
Helixi99 – 11416Combined sources
Helixi117 – 1259Combined sources
Helixi131 – 1333Combined sources
Beta strandi143 – 1475Combined sources
Helixi151 – 16111Combined sources
Turni162 – 1643Combined sources
Beta strandi166 – 1705Combined sources
Helixi176 – 1827Combined sources
Helixi189 – 1957Combined sources
Beta strandi197 – 2015Combined sources
Turni207 – 2115Combined sources
Helixi215 – 2184Combined sources
Beta strandi226 – 2294Combined sources
Helixi238 – 2469Combined sources
Beta strandi248 – 2503Combined sources
Beta strandi252 – 2576Combined sources
Beta strandi259 – 2624Combined sources
Helixi267 – 2704Combined sources
Beta strandi274 – 2763Combined sources
Helixi285 – 30319Combined sources
Turni321 – 3255Combined sources
Helixi326 – 33914Combined sources
Beta strandi341 – 3433Combined sources
Beta strandi346 – 3549Combined sources
Helixi355 – 3584Combined sources
Helixi362 – 37211Combined sources
Helixi374 – 3763Combined sources
Helixi386 – 3938Combined sources
Beta strandi396 – 4038Combined sources
Beta strandi406 – 41712Combined sources
Beta strandi423 – 4319Combined sources
Turni432 – 4354Combined sources
Beta strandi436 – 4427Combined sources
Beta strandi445 – 4517Combined sources
Beta strandi453 – 4619Combined sources
Helixi466 – 47611Combined sources
Beta strandi481 – 4888Combined sources
Beta strandi490 – 4934Combined sources
Beta strandi495 – 5039Combined sources
Helixi507 – 51711Combined sources
Beta strandi519 – 5268Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1YGYX-ray2.30A/B2-528[»]
3DC2X-ray2.70A/B2-528[»]
3DDNX-ray2.40A/B2-528[»]
ProteinModelPortaliP9WNX3.
SMRiP9WNX3. Positions 2-528.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini455 – 52773ACTPROSITE-ProRule annotationAdd
BLAST

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
EntryMethodResolution (Å)ChainPositionsPDBsum
1YGYX-ray2.30A/B2-528[»]
3DC2X-ray2.70A/B2-528[»]
3DDNX-ray2.40A/B2-528[»]
ProteinModelPortaliP9WNX3.
SMRiP9WNX3. Positions 2-528.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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.

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: January 20, 2016
This is version 18 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.