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Protein

4-hydroxy-tetrahydrodipicolinate synthase

Gene

dapA

Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Status
Reviewed-Annotation score: Annotation score: 5 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

Enzyme regulationi

Is not inhibited by (S)-lysine, in contrast to E.coli DapA.1 Publication

Kineticsi

kcat is 136 sec(-1) and 465 sec (-1) at 30 and 45 degrees Celsius, respectively.1 Publication

  1. KM=0.053 mM for pyruvate (at 30 degrees Celsius, PubMed:16872276)2 Publications
  2. KM=0.08 mM for pyruvate (at 30 degrees Celsius, PubMed:21803176)2 Publications
  3. KM=0.15 mM for pyruvate (at 45 degrees Celsius, PubMed:21803176)2 Publications
  4. KM=0.16 mM for L-aspartate-4-semialdehyde (at 30 degrees Celsius, PubMed:16872276)2 Publications
  5. KM=0.23 mM for L-aspartate-4-semialdehyde (at 30 degrees Celsius, PubMed:21803176)2 Publications
  6. KM=0.36 mM for L-aspartate-4-semialdehyde (at 45 degrees Celsius, PubMed:21803176)2 Publications
  1. Vmax=1.01 µmol/sec/mg enzyme (at 30 degrees Celsius, PubMed:16872276)2 Publications

Temperature dependencei

Highly thermostable. Retains over 60% of the activity after 7 hours incubation at 90 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. no protein annotated in this organism
  2. no protein annotated in this organism
  3. Dihydrodipicolinate synthase (Tmari_1529), 4-hydroxy-tetrahydrodipicolinate synthase (dapA)
  4. 4-hydroxy-tetrahydrodipicolinate reductase (Tmari_1528), 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
Sitei43 – 431Part of a proton relay during catalysisUniRule annotation
Binding sitei44 – 441PyruvateUniRule annotation
Sitei106 – 1061Part of a proton relay during catalysisUniRule annotation
Active sitei132 – 1321Proton donor/acceptorUniRule annotation
Active sitei161 – 1611Schiff-base intermediate with substrateUniRule annotation
Binding sitei206 – 2061Pyruvate; 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. 6331.
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:TM_1521
OrganismiThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Taxonomic identifieri243274 [NCBI]
Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermotoga
Proteomesi
  • UP000008183 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi166 – 1683DID → AAA: Exists as a monomer in solution. Decreased activity and substrate affinity. Reduced thermal stability. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 2942944-hydroxy-tetrahydrodipicolinate synthasePRO_0000103175Add
BLAST

Interactioni

Subunit structurei

Homotetramer; dimer of dimers.UniRule annotation2 Publications

Protein-protein interaction databases

STRINGi243274.TM1521.

Structurei

Secondary structure

1
294
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 86Combined sources
Helixi20 – 3213Combined sources
Beta strandi37 – 426Combined sources
Helixi43 – 453Combined sources
Helixi47 – 493Combined sources
Helixi52 – 6615Combined sources
Beta strandi72 – 754Combined sources
Helixi81 – 9414Combined sources
Beta strandi97 – 1026Combined sources
Helixi111 – 12212Combined sources
Beta strandi129 – 1335Combined sources
Helixi135 – 1384Combined sources
Helixi144 – 15310Combined sources
Beta strandi157 – 1626Combined sources
Helixi167 – 18014Combined sources
Beta strandi185 – 1906Combined sources
Helixi191 – 1933Combined sources
Helixi194 – 2007Combined sources
Beta strandi204 – 2085Combined sources
Helixi209 – 2113Combined sources
Helixi214 – 22512Combined sources
Helixi229 – 24517Combined sources
Beta strandi248 – 2503Combined sources
Helixi253 – 2619Combined sources
Helixi278 – 29013Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1O5KX-ray1.80A/B1-294[»]
3PB0X-ray2.00A/B/C/D1-294[»]
3PB2X-ray1.90A/B/C/D/E/F1-294[»]
ProteinModelPortaliQ9X1K9.
SMRiQ9X1K9. Positions 1-294.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9X1K9.

Family & Domainsi

Sequence similaritiesi

Belongs to the DapA family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105CDP. Bacteria.
COG0329. LUCA.
InParanoidiQ9X1K9.
KOiK01714.
OMAiGMDACVP.
OrthoDBiEOG6W7235.

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.

Q9X1K9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFRGVGTAIV TPFKNGELDL ESYERLVRYQ LENGVNALIV LGTTGESPTV
60 70 80 90 100
NEDEREKLVS RTLEIVDGKI PVIVGAGTNS TEKTLKLVKQ AEKLGANGVL
110 120 130 140 150
VVTPYYNKPT QEGLYQHYKY ISERTDLGIV VYNVPGRTGV NVLPETAARI
160 170 180 190 200
AADLKNVVGI KEANPDIDQI DRTVSLTKQA RSDFMVWSGN DDRTFYLLCA
210 220 230 240 250
GGDGVISVVS NVAPKQMVEL CAEYFSGNLE KSREVHRKLR PLMKALFVET
260 270 280 290
NPIPVKAALN LMGFIENELR LPLVPASEKT VELLRNVLKE SGLL
Length:294
Mass (Da):32,390
Last modified:November 1, 1999 - v1
Checksum:i64C93C64734A351D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD36588.1.
PIRiB72246.
RefSeqiNP_229321.1. NC_000853.1.
WP_004081879.1. NZ_CP011107.1.

Genome annotation databases

EnsemblBacteriaiAAD36588; AAD36588; TM_1521.
GeneIDi897344.
KEGGitma:TM1521.
PATRICi23938000. VBITheMar51294_1538.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD36588.1.
PIRiB72246.
RefSeqiNP_229321.1. NC_000853.1.
WP_004081879.1. NZ_CP011107.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1O5KX-ray1.80A/B1-294[»]
3PB0X-ray2.00A/B/C/D1-294[»]
3PB2X-ray1.90A/B/C/D/E/F1-294[»]
ProteinModelPortaliQ9X1K9.
SMRiQ9X1K9. Positions 1-294.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243274.TM1521.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD36588; AAD36588; TM_1521.
GeneIDi897344.
KEGGitma:TM1521.
PATRICi23938000. VBITheMar51294_1538.

Phylogenomic databases

eggNOGiENOG4105CDP. Bacteria.
COG0329. LUCA.
InParanoidiQ9X1K9.
KOiK01714.
OMAiGMDACVP.
OrthoDBiEOG6W7235.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00017.
BRENDAi4.3.3.7. 6331.

Miscellaneous databases

EvolutionaryTraceiQ9X1K9.

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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
  2. "Dihydrodipicolinate synthase from Thermotoga maritima."
    Pearce F.G., Perugini M.A., McKerchar H.J., Gerrard J.A.
    Biochem. J. 400:359-366(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS), FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBUNIT.
    Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
  3. "Characterization of monomeric dihydrodipicolinate synthase variant reveals the importance of substrate binding in optimizing oligomerization."
    Pearce F.G., Dobson R.C., Jameson G.B., Perugini M.A., Gerrard J.A.
    Biochim. Biophys. Acta 1814:1900-1909(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF MUTANT ALA-166/ALA-167/ALA-168 AND MUTANT ALA-233/ALA-237, MUTAGENESIS OF 166-ASP--ASP-168, KINETIC PARAMETERS, SUBUNIT.
    Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.

Entry informationi

Entry nameiDAPA_THEMA
AccessioniPrimary (citable) accession number: Q9X1K9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1999
Last modified: May 11, 2016
This is version 119 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.