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Protein

4-hydroxy-tetrahydrodipicolinate reductase

Gene

dapB

Organism
Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate.UniRule annotation

Catalytic activityi

(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)+ + H2O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H.UniRule annotation

Pathwayi: L-lysine biosynthesis via DAP pathway

This protein is involved in step 4 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. Aspartate-semialdehyde dehydrogenase (asd)
  3. 4-hydroxy-tetrahydrodipicolinate synthase (dapA-1), 4-hydroxy-tetrahydrodipicolinate synthase (dapA-2)
  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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei36 – 361NADUniRule annotation
Binding sitei37 – 371NADPUniRule annotation
Active sitei156 – 1561Proton donor/acceptorUniRule annotation
Binding sitei157 – 1571SubstrateUniRule annotation
Active sitei160 – 1601Proton donorUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi10 – 156NAD(P)UniRule annotation
Nucleotide bindingi99 – 1013NAD(P)UniRule annotation
Nucleotide bindingi123 – 1264NAD(P)UniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Amino-acid biosynthesis, Diaminopimelate biosynthesis, Lysine biosynthesis

Keywords - Ligandi

NAD, NADP

Enzyme and pathway databases

BioCyciBTHA271848:GJMY-1208-MONOMER.
UniPathwayiUPA00034; UER00018.

Names & Taxonomyi

Protein namesi
Recommended name:
4-hydroxy-tetrahydrodipicolinate reductaseUniRule annotation (EC:1.17.1.8UniRule annotation)
Short name:
HTPA reductaseUniRule annotation
Gene namesi
Name:dapBUniRule annotation
Ordered Locus Names:BTH_I1208
OrganismiBurkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264)
Taxonomic identifieri271848 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeBurkholderiapseudomallei group
Proteomesi
  • UP000001930 Componenti: Chromosome I

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 – 2682684-hydroxy-tetrahydrodipicolinate reductasePRO_1000008547Add
BLAST

Structurei

Secondary structure

1
268
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 107Combined sources
Helixi14 – 2512Combined sources
Beta strandi29 – 357Combined sources
Turni41 – 444Combined sources
Turni47 – 526Combined sources
Helixi63 – 697Combined sources
Beta strandi71 – 755Combined sources
Helixi79 – 9214Combined sources
Beta strandi95 – 984Combined sources
Helixi105 – 11410Combined sources
Turni115 – 1173Combined sources
Beta strandi118 – 1225Combined sources
Helixi128 – 14316Combined sources
Beta strandi145 – 1473Combined sources
Beta strandi149 – 1568Combined sources
Beta strandi162 – 1643Combined sources
Helixi166 – 17712Combined sources
Turni178 – 1803Combined sources
Helixi183 – 1864Combined sources
Beta strandi187 – 1893Combined sources
Beta strandi203 – 2097Combined sources
Beta strandi215 – 2228Combined sources
Beta strandi224 – 23411Combined sources
Helixi238 – 25215Combined sources
Beta strandi255 – 2595Combined sources
Helixi261 – 2644Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4F3YX-ray2.10A/B1-268[»]
ProteinModelPortaliQ2SZ94.
SMRiQ2SZ94. Positions 2-268.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni166 – 1672Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the DapB family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000227153.
KOiK00215.
OMAiEAHHRMK.
OrthoDBiEOG6SV5DS.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00102. DapB.
InterProiIPR022663. DapB_C.
IPR000846. DapB_N.
IPR022664. DapB_N_CS.
IPR023940. DHDPR_bac.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PANTHERiPTHR20836. PTHR20836. 1 hit.
PfamiPF05173. DapB_C. 1 hit.
PF01113. DapB_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000161. DHPR. 1 hit.
SUPFAMiSSF51735. SSF51735. 2 hits.
TIGRFAMsiTIGR00036. dapB. 1 hit.
PROSITEiPS01298. DAPB. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q2SZ94-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSMKIAIAG ASGRMGRMLI EAVLAAPDAT LVGALDRTGS PQLGQDAGAF
60 70 80 90 100
LGKQTGVALT DDIERVCAEA DYLIDFTLPE GTLVHLDAAL RHDVKLVIGT
110 120 130 140 150
TGFSEPQKAQ LRAAGEKIAL VFSANMSVGV NVTMKLLEFA AKQFAQGYDI
160 170 180 190 200
EIIEAHHRHK VDAPSGTALM MGETIAAATG RSLDDCAVYG RHGVTGERDP
210 220 230 240 250
STIGFSAIRG GDIVGDHTVL FAGIGERIEI THKSASRVSY AQGALRAARF
260
LAGRDAGFFD MQDVLGLR
Length:268
Mass (Da):28,213
Last modified:January 24, 2006 - v1
Checksum:i77D8AB40058EE3F8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000086 Genomic DNA. Translation: ABC36898.1.

Genome annotation databases

EnsemblBacteriaiABC36898; ABC36898; BTH_I1208.
KEGGibte:BTH_I1208.
PATRICi19305310. VBIBurTha36512_3964.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000086 Genomic DNA. Translation: ABC36898.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4F3YX-ray2.10A/B1-268[»]
ProteinModelPortaliQ2SZ94.
SMRiQ2SZ94. Positions 2-268.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABC36898; ABC36898; BTH_I1208.
KEGGibte:BTH_I1208.
PATRICi19305310. VBIBurTha36512_3964.

Phylogenomic databases

HOGENOMiHOG000227153.
KOiK00215.
OMAiEAHHRMK.
OrthoDBiEOG6SV5DS.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00018.
BioCyciBTHA271848:GJMY-1208-MONOMER.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00102. DapB.
InterProiIPR022663. DapB_C.
IPR000846. DapB_N.
IPR022664. DapB_N_CS.
IPR023940. DHDPR_bac.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PANTHERiPTHR20836. PTHR20836. 1 hit.
PfamiPF05173. DapB_C. 1 hit.
PF01113. DapB_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000161. DHPR. 1 hit.
SUPFAMiSSF51735. SSF51735. 2 hits.
TIGRFAMsiTIGR00036. dapB. 1 hit.
PROSITEiPS01298. DAPB. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Bacterial genome adaptation to niches: divergence of the potential virulence genes in three Burkholderia species of different survival strategies."
    Kim H.S., Schell M.A., Yu Y., Ulrich R.L., Sarria S.H., Nierman W.C., DeShazer D.
    BMC Genomics 6:174-174(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700388 / DSM 13276 / CIP 106301 / E264.

Entry informationi

Entry nameiDAPB_BURTA
AccessioniPrimary (citable) accession number: Q2SZ94
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: January 24, 2006
Last modified: July 6, 2016
This is version 79 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 reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown in E.coli that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction.Curated

Keywords - Technical termi

3D-structure, Complete 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.