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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

Manual assertion based on experiment ini

  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. Aspartokinase (TM_1518)
  2. no protein annotated in this organism
  3. 4-hydroxy-tetrahydrodipicolinate synthase (dapA), 4-hydroxy-tetrahydrodipicolinate synthase (dapA)
  4. 4-hydroxy-tetrahydrodipicolinate reductase (dapB), 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
Sitei43Part of a proton relay during catalysisUniRule annotation1
Binding sitei44PyruvateUniRule annotation1
Sitei106Part of a proton relay during catalysisUniRule annotation1
Active sitei132Proton donor/acceptorUniRule annotation1
Active sitei161Schiff-base intermediate with substrateUniRule annotation1
Binding sitei206Pyruvate; 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. 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)DescriptionActionsGraphical viewLength
Mutagenesisi166 – 168DID → AAA: Exists as a monomer in solution. Decreased activity and substrate affinity. Reduced thermal stability. 1 Publication3

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001031751 – 2944-hydroxy-tetrahydrodipicolinate synthaseAdd BLAST294

Interactioni

Subunit structurei

Homotetramer; dimer of dimers.UniRule annotation2 Publications

Protein-protein interaction databases

STRINGi243274.TM1521.

Structurei

Secondary structure

1294
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 8Combined sources6
Helixi20 – 32Combined sources13
Beta strandi37 – 42Combined sources6
Helixi43 – 45Combined sources3
Helixi47 – 49Combined sources3
Helixi52 – 66Combined sources15
Beta strandi72 – 75Combined sources4
Helixi81 – 94Combined sources14
Beta strandi97 – 102Combined sources6
Helixi111 – 122Combined sources12
Beta strandi129 – 133Combined sources5
Helixi135 – 138Combined sources4
Helixi144 – 153Combined sources10
Beta strandi157 – 162Combined sources6
Helixi167 – 180Combined sources14
Beta strandi185 – 190Combined sources6
Helixi191 – 193Combined sources3
Helixi194 – 200Combined sources7
Beta strandi204 – 208Combined sources5
Helixi209 – 211Combined sources3
Helixi214 – 225Combined sources12
Helixi229 – 245Combined sources17
Beta strandi248 – 250Combined sources3
Helixi253 – 261Combined sources9
Helixi278 – 290Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
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.

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.

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
PDB 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.
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.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00017.
BRENDAi4.3.3.7. 6331.

Miscellaneous databases

EvolutionaryTraceiQ9X1K9.

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_THEMA
AccessioniPrimary (citable) accession number: Q9X1K9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1999
Last modified: November 2, 2016
This is version 122 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.