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Protein

4-hydroxy-tetrahydrodipicolinate synthase

Gene

dapA

Organism
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).UniRule annotation

Catalytic activityi

Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H2O.UniRule annotation

Pathwayi: L-lysine biosynthesis via DAP pathway

This protein is involved in step 3 of the subpathway that synthesizes (S)-tetrahydrodipicolinate from L-aspartate.UniRule annotation
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. Aspartokinase (lysC)
  2. Aspartate-semialdehyde dehydrogenase (asd)
  3. 4-hydroxy-tetrahydrodipicolinate synthase (dapA)
  4. 4-hydroxy-tetrahydrodipicolinate reductase (dapB)
This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, 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 (S)-tetrahydrodipicolinate from L-aspartate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei56Part of a proton relay during catalysisUniRule annotation1
Binding sitei57PyruvateUniRule annotation1
Sitei119Part of a proton relay during catalysisUniRule annotation1
Active sitei145Proton donor/acceptorUniRule annotation1
Active sitei173Schiff-base intermediate with substrateUniRule annotation1
Binding sitei213Pyruvate; via carbonyl oxygenUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Amino-acid biosynthesis, Diaminopimelate biosynthesis, Lysine biosynthesis

Keywords - Ligandi

Schiff base

Enzyme and pathway databases

BioCyciCORYNE:G18NG-11563-MONOMER.
MetaCyc:MONOMER-6444.
BRENDAi4.3.3.7. 960.
UniPathwayiUPA00034; UER00017.

Names & Taxonomyi

Protein namesi
Recommended name:
4-hydroxy-tetrahydrodipicolinate synthaseUniRule annotation (EC:4.3.3.7UniRule annotation)
Short name:
HTPA synthaseUniRule annotation
Gene namesi
Name:dapAUniRule annotation
Ordered Locus Names:Cgl1971, cg2161
OrganismiCorynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Taxonomic identifieri196627 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesCorynebacteriaceaeCorynebacterium
Proteomesi
  • UP000000582 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001031091 – 3014-hydroxy-tetrahydrodipicolinate synthaseAdd BLAST301

Proteomic databases

PRIDEiP19808.

2D gel databases

World-2DPAGE0001:P19808.

Interactioni

Subunit structurei

Homotetramer; dimer of dimers.UniRule annotation

Protein-protein interaction databases

STRINGi196627.cg2161.

Structurei

Secondary structure

1301
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi11 – 14Combined sources4
Beta strandi16 – 20Combined sources5
Helixi33 – 45Combined sources13
Beta strandi50 – 55Combined sources6
Turni56 – 62Combined sources7
Helixi65 – 79Combined sources15
Turni80 – 82Combined sources3
Beta strandi83 – 88Combined sources6
Helixi94 – 106Combined sources13
Beta strandi110 – 115Combined sources6
Helixi124 – 137Combined sources14
Beta strandi142 – 146Combined sources5
Helixi148 – 151Combined sources4
Helixi157 – 163Combined sources7
Beta strandi169 – 174Combined sources6
Helixi179 – 189Combined sources11
Beta strandi192 – 195Combined sources4
Helixi198 – 200Combined sources3
Helixi201 – 206Combined sources6
Beta strandi211 – 215Combined sources5
Helixi216 – 218Combined sources3
Helixi221 – 233Combined sources13
Helixi236 – 245Combined sources10
Helixi247 – 256Combined sources10
Helixi258 – 268Combined sources11
Helixi285 – 297Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3CPRX-ray2.20A/B2-301[»]
ProteinModelPortaliP19808.
SMRiP19808.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP19808.

Family & Domainsi

Sequence similaritiesi

Belongs to the DapA family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105CDP. Bacteria.
COG0329. LUCA.
HOGENOMiHOG000173604.
KOiK01714.
OMAiMDFTSNG.

Family and domain databases

CDDicd00950. DHDPS. 1 hit.
Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00418. DapA. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR005263. DapA.
IPR002220. DapA-like.
IPR020625. Schiff_base-form_aldolases_AS.
IPR020624. Schiff_base-form_aldolases_CS.
[Graphical view]
PANTHERiPTHR12128. PTHR12128. 1 hit.
PfamiPF00701. DHDPS. 1 hit.
[Graphical view]
PIRSFiPIRSF001365. DHDPS. 1 hit.
PRINTSiPR00146. DHPICSNTHASE.
SMARTiSM01130. DHDPS. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00674. dapA. 1 hit.
PROSITEiPS00665. DHDPS_1. 1 hit.
PS00666. DHDPS_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P19808-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTGLTAKTG VEHFGTVGVA MVTPFTESGD IDIAAGREVA AYLVDKGLDS
60 70 80 90 100
LVLAGTTGES PTTTAAEKLE LLKAVREEVG DRAKLIAGVG TNNTRTSVEL
110 120 130 140 150
AEAAASAGAD GLLVVTPYYS KPSQEGLLAH FGAIAAATEV PICLYDIPGR
160 170 180 190 200
SGIPIESDTM RRLSELPTIL AVKDAKGDLV AATSLIKETG LAWYSGDDPL
210 220 230 240 250
NLVWLALGGS GFISVIGHAA PTALRELYTS FEEGDLVRAR EINAKLSPLV
260 270 280 290 300
AAQGRLGGVS LAKAALRLQG INVGDPRLPI MAPNEQELEA LREDMKKAGV

L
Length:301
Mass (Da):31,262
Last modified:July 11, 2002 - v2
Checksum:i6B803A4E829393B3
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti266L → S in CAA37940 (PubMed:2129555).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X53993 Genomic DNA. Translation: CAA37940.1.
Z21502 Genomic DNA. Translation: CAA79714.1.
BA000036 Genomic DNA. Translation: BAB99364.1.
BX927153 Genomic DNA. Translation: CAF20312.1.
PIRiC40626.
RefSeqiNP_601177.1. NC_003450.3.
WP_011014792.1. NC_006958.1.

Genome annotation databases

EnsemblBacteriaiBAB99364; BAB99364; BAB99364.
CAF20312; CAF20312; cg2161.
GeneIDi1019928.
KEGGicgb:cg2161.
cgl:NCgl1896.
PATRICi21495944. VBICorGlu203724_1908.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X53993 Genomic DNA. Translation: CAA37940.1.
Z21502 Genomic DNA. Translation: CAA79714.1.
BA000036 Genomic DNA. Translation: BAB99364.1.
BX927153 Genomic DNA. Translation: CAF20312.1.
PIRiC40626.
RefSeqiNP_601177.1. NC_003450.3.
WP_011014792.1. NC_006958.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3CPRX-ray2.20A/B2-301[»]
ProteinModelPortaliP19808.
SMRiP19808.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi196627.cg2161.

2D gel databases

World-2DPAGE0001:P19808.

Proteomic databases

PRIDEiP19808.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAB99364; BAB99364; BAB99364.
CAF20312; CAF20312; cg2161.
GeneIDi1019928.
KEGGicgb:cg2161.
cgl:NCgl1896.
PATRICi21495944. VBICorGlu203724_1908.

Phylogenomic databases

eggNOGiENOG4105CDP. Bacteria.
COG0329. LUCA.
HOGENOMiHOG000173604.
KOiK01714.
OMAiMDFTSNG.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00017.
BioCyciCORYNE:G18NG-11563-MONOMER.
MetaCyc:MONOMER-6444.
BRENDAi4.3.3.7. 960.

Miscellaneous databases

EvolutionaryTraceiP19808.

Family and domain databases

CDDicd00950. DHDPS. 1 hit.
Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00418. DapA. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR005263. DapA.
IPR002220. DapA-like.
IPR020625. Schiff_base-form_aldolases_AS.
IPR020624. Schiff_base-form_aldolases_CS.
[Graphical view]
PANTHERiPTHR12128. PTHR12128. 1 hit.
PfamiPF00701. DHDPS. 1 hit.
[Graphical view]
PIRSFiPIRSF001365. DHDPS. 1 hit.
PRINTSiPR00146. DHPICSNTHASE.
SMARTiSM01130. DHDPS. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00674. dapA. 1 hit.
PROSITEiPS00665. DHDPS_1. 1 hit.
PS00666. DHDPS_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDAPA_CORGL
AccessioniPrimary (citable) accession number: P19808
Secondary accession number(s): P40109
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: July 11, 2002
Last modified: November 2, 2016
This is version 125 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

Was originally thought to be a dihydrodipicolinate synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.