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Protein

4-hydroxy-tetrahydrodipicolinate synthase

Gene

dapA

Organism
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Status
Reviewed-Annotation score: Annotation score: 4 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).1 Publication

Catalytic activityi

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

Kineticsi

  1. KM=0.90 mM for pyruvate1 Publication
  2. KM=0.17 mM for L-aspartate-4-semialdehyde1 Publication
  1. Vmax=0.030 mmol/min/µg enzyme1 Publication

pH dependencei

Optimum pH is 8.0. At pH 9.0 or above, only 30% activity is observed.1 Publication

Temperature dependencei

Optimum temperature is 37 degrees Celsius. The activity decreases slowly when temperatures are reduced from 37 degrees Celsius while the drop in activity is relatively more rapid when temperatures are raised above 37 degrees Celsius. In this case, the activity reduces to almost 30% at 52 degrees Celsius.1 Publication

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
Sitei44Part of a proton relay during catalysisUniRule annotation1
Binding sitei45PyruvateUniRule annotation1
Sitei107Part of a proton relay during catalysisUniRule annotation1
Active sitei133Proton donor/acceptorUniRule annotation1
Active sitei161Schiff-base intermediate with substrateUniRule annotation1
Binding sitei203Pyruvate; 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

BRENDAi4.3.3.7. 5087.
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:PA1010
OrganismiPseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Taxonomic identifieri208964 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
Proteomesi
  • UP000002438 Componenti: Chromosome

Organism-specific databases

PseudoCAPiPA1010.

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_00001031381 – 2924-hydroxy-tetrahydrodipicolinate synthaseAdd BLAST292

Proteomic databases

PaxDbiQ9I4W3.
PRIDEiQ9I4W3.

Interactioni

Subunit structurei

Homodimer.UniRule annotation1 Publication

Protein-protein interaction databases

STRINGi208964.PA1010.

Structurei

Secondary structure

1292
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 8Combined sources5
Helixi21 – 34Combined sources14
Beta strandi38 – 43Combined sources6
Helixi44 – 46Combined sources3
Helixi48 – 50Combined sources3
Helixi53 – 67Combined sources15
Beta strandi73 – 76Combined sources4
Helixi82 – 94Combined sources13
Beta strandi98 – 103Combined sources6
Turni106 – 108Combined sources3
Helixi112 – 125Combined sources14
Beta strandi130 – 134Combined sources5
Helixi136 – 139Combined sources4
Helixi145 – 152Combined sources8
Beta strandi157 – 162Combined sources6
Helixi167 – 176Combined sources10
Beta strandi181 – 186Combined sources6
Helixi188 – 190Combined sources3
Helixi191 – 196Combined sources6
Beta strandi201 – 205Combined sources5
Helixi206 – 208Combined sources3
Helixi211 – 222Combined sources12
Helixi226 – 242Combined sources17
Beta strandi245 – 247Combined sources3
Helixi250 – 258Combined sources9
Helixi275 – 277Combined sources3
Helixi278 – 287Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3NOEX-ray2.95A/B1-292[»]
3PS7X-ray2.85A/B1-292[»]
3PUOX-ray2.65A/B1-292[»]
3QZEX-ray1.59A/B/C/D1-292[»]
3S8HX-ray2.70A/B1-292[»]
ProteinModelPortaliQ9I4W3.
SMRiQ9I4W3.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9I4W3.

Family & Domainsi

Sequence similaritiesi

Belongs to the DapA family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105CDP. Bacteria.
COG0329. LUCA.
HOGENOMiHOG000173604.
InParanoidiQ9I4W3.
KOiK01714.
OMAiGMDACVP.
PhylomeDBiQ9I4W3.

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.

Q9I4W3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIAGSMVALV TPFDAQGRLD WDSLAKLVDF HLQEGTNAIV AVGTTGESAT
60 70 80 90 100
LDVEEHIQVI RRVVDQVKGR IPVIAGTGAN STREAVALTE AAKSGGADAC
110 120 130 140 150
LLVTPYYNKP TQEGMYQHFR HIAEAVAIPQ ILYNVPGRTS CDMLPETVER
160 170 180 190 200
LSKVPNIIGI KEATGDLQRA KEVIERVGKD FLVYSGDDAT AVELMLLGGK
210 220 230 240 250
GNISVTANVA PRAMSDLCAA AMRGDAAAAR AINDRLMPLH KALFIESNPI
260 270 280 290
PVKWALHEMG LIPEGIRLPL TWLSPRCHEP LRQAMRQTGV LA
Length:292
Mass (Da):31,449
Last modified:March 1, 2001 - v1
Checksum:i8E611F4C2A4A60FE
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti234D → E in ACZ37227 (PubMed:21396954).Curated1
Sequence conflicti276R → H in ACZ37227 (PubMed:21396954).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
GU166748 Genomic DNA. Translation: ACZ37227.1.
AE004091 Genomic DNA. Translation: AAG04399.1.
PIRiC83520.
RefSeqiNP_249701.1. NC_002516.2.
WP_003086270.1. NZ_ASJY01000132.1.

Genome annotation databases

EnsemblBacteriaiAAG04399; AAG04399; PA1010.
GeneIDi879525.
KEGGipae:PA1010.
PATRICi19836310. VBIPseAer58763_1042.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
GU166748 Genomic DNA. Translation: ACZ37227.1.
AE004091 Genomic DNA. Translation: AAG04399.1.
PIRiC83520.
RefSeqiNP_249701.1. NC_002516.2.
WP_003086270.1. NZ_ASJY01000132.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3NOEX-ray2.95A/B1-292[»]
3PS7X-ray2.85A/B1-292[»]
3PUOX-ray2.65A/B1-292[»]
3QZEX-ray1.59A/B/C/D1-292[»]
3S8HX-ray2.70A/B1-292[»]
ProteinModelPortaliQ9I4W3.
SMRiQ9I4W3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi208964.PA1010.

Proteomic databases

PaxDbiQ9I4W3.
PRIDEiQ9I4W3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAG04399; AAG04399; PA1010.
GeneIDi879525.
KEGGipae:PA1010.
PATRICi19836310. VBIPseAer58763_1042.

Organism-specific databases

PseudoCAPiPA1010.

Phylogenomic databases

eggNOGiENOG4105CDP. Bacteria.
COG0329. LUCA.
HOGENOMiHOG000173604.
InParanoidiQ9I4W3.
KOiK01714.
OMAiGMDACVP.
PhylomeDBiQ9I4W3.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00017.
BRENDAi4.3.3.7. 5087.

Miscellaneous databases

EvolutionaryTraceiQ9I4W3.

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_PSEAE
AccessioniPrimary (citable) accession number: Q9I4W3
Secondary accession number(s): D1MH64
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 20, 2001
Last sequence update: March 1, 2001
Last modified: November 2, 2016
This is version 103 of the entry and version 1 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.