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Protein

4-hydroxy-tetrahydrodipicolinate synthase

Gene

dapA

Organism
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
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)LengthDescriptionGraphical viewFeature identifierActions
Sitei44 – 441Part of a proton relay during catalysisUniRule annotation
Binding sitei45 – 451PyruvateUniRule annotation
Sitei107 – 1071Part of a proton relay during catalysisUniRule annotation
Active sitei133 – 1331Proton donor/acceptorUniRule annotation
Active sitei161 – 1611Schiff-base intermediate with substrateUniRule annotation
Binding sitei203 – 2031Pyruvate; via carbonyl oxygenUniRule annotation

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 / PAO1 / 1C / PRS 101 / LMG 12228)
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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 2922924-hydroxy-tetrahydrodipicolinate synthasePRO_0000103138Add
BLAST

Proteomic databases

PaxDbiQ9I4W3.
PRIDEiQ9I4W3.

Interactioni

Subunit structurei

Homodimer.UniRule annotation1 Publication

Protein-protein interaction databases

STRINGi208964.PA1010.

Structurei

Secondary structure

1
292
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 85Combined sources
Helixi21 – 3414Combined sources
Beta strandi38 – 436Combined sources
Helixi44 – 463Combined sources
Helixi48 – 503Combined sources
Helixi53 – 6715Combined sources
Beta strandi73 – 764Combined sources
Helixi82 – 9413Combined sources
Beta strandi98 – 1036Combined sources
Turni106 – 1083Combined sources
Helixi112 – 12514Combined sources
Beta strandi130 – 1345Combined sources
Helixi136 – 1394Combined sources
Helixi145 – 1528Combined sources
Beta strandi157 – 1626Combined sources
Helixi167 – 17610Combined sources
Beta strandi181 – 1866Combined sources
Helixi188 – 1903Combined sources
Helixi191 – 1966Combined sources
Beta strandi201 – 2055Combined sources
Helixi206 – 2083Combined sources
Helixi211 – 22212Combined sources
Helixi226 – 24217Combined sources
Beta strandi245 – 2473Combined sources
Helixi250 – 2589Combined sources
Helixi275 – 2773Combined sources
Helixi278 – 28710Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-291.
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.
OrthoDBiEOG6W7235.
PhylomeDBiQ9I4W3.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00418. DapA.
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti234 – 2341D → E in ACZ37227 (PubMed:21396954).Curated
Sequence conflicti276 – 2761R → H in ACZ37227 (PubMed:21396954).Curated

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
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. Positions 1-291.
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.
OrthoDBiEOG6W7235.
PhylomeDBiQ9I4W3.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00017.
BRENDAi4.3.3.7. 5087.

Miscellaneous databases

EvolutionaryTraceiQ9I4W3.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00418. DapA.
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...

Publicationsi

« Hide 'large scale' publications
  1. "Biochemical studies and crystal structure determination of dihydrodipicolinate synthase from Pseudomonas aeruginosa."
    Kaur N., Gautam A., Kumar S., Singh A., Singh N., Sharma S., Sharma R., Tewari R., Singh T.P.
    Int. J. Biol. Macromol. 48:779-787(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH (S)-LYSINE, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228.
  3. "High resolution structure of DapA (PA1010) from Pseudomonas aeruginosa PAO1."
    Schnell R., Sandalova T., Schneider G.
    Submitted (MAR-2011) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.59 ANGSTROMS).
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228.
  4. "Structure of dihydrodipicolinate synthase complexed with 3-hydroxypropanoic acid (HPA) at 2.70 A resolution."
    Kumar M., Kaur N., Kumar S., Sinha M., Kaur P., Sharma S., Singh T.P.
    Submitted (MAY-2011) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS).

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: May 11, 2016
This is version 100 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.