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Protein

4-hydroxy-tetrahydrodipicolinate synthase

Gene

dapA

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
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. Probable aspartokinase (MJ0571)
  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
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 sitei201 – 2011Pyruvate; 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. 3260.
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:MJ0244
OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Taxonomic identifieri243232 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
Proteomesi
  • UP000000805 Componenti: Chromosome

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 – 2892894-hydroxy-tetrahydrodipicolinate synthasePRO_0000103197Add
BLAST

Interactioni

Subunit structurei

Homotetramer; dimer of dimers.UniRule annotation1 Publication

Protein-protein interaction databases

STRINGi243232.MJ_0244.

Structurei

Secondary structure

1
289
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 85Combined sources
Helixi20 – 3213Combined sources
Beta strandi36 – 427Combined sources
Turni43 – 464Combined sources
Helixi47 – 493Combined sources
Helixi52 – 6615Combined sources
Beta strandi69 – 757Combined sources
Helixi81 – 9414Combined sources
Beta strandi97 – 1026Combined sources
Helixi111 – 12414Combined sources
Beta strandi129 – 1335Combined sources
Helixi135 – 1384Combined sources
Helixi144 – 15310Combined sources
Beta strandi157 – 1626Combined sources
Helixi168 – 1769Combined sources
Beta strandi179 – 1846Combined sources
Helixi186 – 1883Combined sources
Helixi189 – 1946Combined sources
Beta strandi199 – 2035Combined sources
Helixi204 – 2063Combined sources
Helixi209 – 22113Combined sources
Helixi224 – 24017Combined sources
Beta strandi243 – 2453Combined sources
Helixi248 – 2569Combined sources
Helixi273 – 28513Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2YXGX-ray2.20A/B/C/D1-289[»]
ProteinModelPortaliQ57695.
SMRiQ57695. Positions 1-289.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ57695.

Family & Domainsi

Sequence similaritiesi

Belongs to the DapA family.UniRule annotation

Phylogenomic databases

eggNOGiarCOG04172. Archaea.
COG0329. LUCA.
InParanoidiQ57695.
KOiK01714.
OMAiGMDACVP.
PhylomeDBiQ57695.

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.

Q57695-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFKGVYPAII TPFKNKEVDF DGLEENINFL IENGVSGIVA VGTTGESPTL
60 70 80 90 100
SHEEHKKVIE KVVDVVNGRV QVIAGAGSNC TEEAIELSVF AEDVGADAVL
110 120 130 140 150
SITPYYNKPT QEGLRKHFGK VAESINLPIV LYNVPSRTAV NLEPKTVKLL
160 170 180 190 200
AEEYSNISAV KEANPNLSQV SELIHDAKIT VLSGNDELTL PIIALGGKGV
210 220 230 240 250
ISVVANIVPK EFVEMVNYAL EGDFEKAREI HYKLFPLMKA MFIETNPIPV
260 270 280
KTALNMMGRP AGELRLPLCE MSEEHKKILE NVLKDLGLI
Length:289
Mass (Da):31,580
Last modified:November 1, 1996 - v1
Checksum:i34CD8619C4A53CCA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB98232.1.
PIRiE64330.

Genome annotation databases

EnsemblBacteriaiAAB98232; AAB98232; MJ_0244.
KEGGimja:MJ_0244.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB98232.1.
PIRiE64330.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2YXGX-ray2.20A/B/C/D1-289[»]
ProteinModelPortaliQ57695.
SMRiQ57695. Positions 1-289.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243232.MJ_0244.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB98232; AAB98232; MJ_0244.
KEGGimja:MJ_0244.

Phylogenomic databases

eggNOGiarCOG04172. Archaea.
COG0329. LUCA.
InParanoidiQ57695.
KOiK01714.
OMAiGMDACVP.
PhylomeDBiQ57695.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00017.
BRENDAi4.3.3.7. 3260.

Miscellaneous databases

EvolutionaryTraceiQ57695.

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 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
  2. Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), SUBUNIT.
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.

Entry informationi

Entry nameiDAPA_METJA
AccessioniPrimary (citable) accession number: Q57695
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: May 11, 2016
This is version 102 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. Methanococcus jannaschii
    Methanococcus jannaschii: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.