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P04036

- DAPB_ECOLI

UniProt

P04036 - DAPB_ECOLI

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Protein

4-hydroxy-tetrahydrodipicolinate reductase

Gene

dapB

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. Can use both NADH and NADPH as a reductant, with NADH being twice as effective as NADPH.2 PublicationsUniRule 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.1 PublicationUniRule annotation

Enzyme regulationi

Is inhibited by 2,6-pyridine dicarboxylate (2,6-PDC or picolinate).1 Publication

Kineticsi

  1. KM=1.6 µM for NADH2 Publications
  2. KM=8 µM for NADPH2 Publications

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei38 – 381NAD1 PublicationUniRule annotation
Binding sitei39 – 391NADP2 PublicationsUniRule annotation
Active sitei159 – 1591Proton donor/acceptor
Binding sitei160 – 1601Substrate
Active sitei163 – 1631Proton donor

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi12 – 176NAD(P)1 PublicationUniRule annotation
Nucleotide bindingi102 – 1043NAD(P)1 PublicationUniRule annotation
Nucleotide bindingi126 – 1294NAD(P)1 PublicationUniRule annotation

GO - Molecular functioni

  1. 4-hydroxy-tetrahydrodipicolinate reductase Source: EcoCyc
  2. identical protein binding Source: EcoCyc
  3. NAD binding Source: UniProtKB-HAMAP
  4. NADPH binding Source: InterPro
  5. oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor Source: UniProtKB-HAMAP

GO - Biological processi

  1. cellular amino acid biosynthetic process Source: EcoliWiki
  2. diaminopimelate biosynthetic process Source: EcoliWiki
  3. lysine biosynthetic process via diaminopimelate Source: UniProtKB-HAMAP
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

BioCyciEcoCyc:DIHYDROPICRED-MONOMER.
ECOL316407:JW0029-MONOMER.
MetaCyc:DIHYDROPICRED-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:b0031, JW0029
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10206. dapB.

Subcellular locationi

GO - Cellular componenti

  1. cytosol Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi159 – 1591H → A or Q: 135 to 200-fold reduction in catalytic activity. 1 Publication
Mutagenesisi163 – 1631K → A, C or Q: 625 to 830-fold reduction in catalytic activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 2732734-hydroxy-tetrahydrodipicolinate reductasePRO_0000141437Add
BLAST

Proteomic databases

PaxDbiP04036.
PRIDEiP04036.

2D gel databases

SWISS-2DPAGEP04036.

Expressioni

Inductioni

Expression of dapB is up-regulated by ArgP and is repressed by lysine that prevents the binding of the ArgP activator. Thus, ArgP contributes to enhanced transcription of dapB when lysine becomes limiting.1 Publication

Gene expression databases

GenevestigatoriP04036.

Interactioni

Subunit structurei

Homotetramer.4 PublicationsUniRule annotation

Protein-protein interaction databases

DIPiDIP-9399N.
IntActiP04036. 1 interaction.
STRINGi511145.b0031.

Structurei

Secondary structure

1
273
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 106
Turni11 – 144
Helixi16 – 2712
Beta strandi32 – 376
Turni44 – 474
Beta strandi52 – 565
Beta strandi62 – 643
Turni67 – 715
Beta strandi74 – 785
Helixi82 – 9413
Beta strandi98 – 1014
Helixi108 – 11710
Turni118 – 1203
Beta strandi123 – 1253
Helixi131 – 14717
Turni148 – 1503
Beta strandi151 – 1599
Beta strandi165 – 1673
Helixi169 – 18113
Helixi186 – 1883
Beta strandi206 – 2127
Beta strandi218 – 2269
Beta strandi229 – 2379
Helixi241 – 25414
Beta strandi259 – 2624
Helixi264 – 2674
Helixi270 – 2723

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ARZX-ray2.60A/B/C/D1-273[»]
1DIHX-ray2.20A1-273[»]
1DRUX-ray2.20A1-273[»]
1DRVX-ray2.20A1-273[»]
1DRWX-ray2.20A1-273[»]
ProteinModelPortaliP04036.
SMRiP04036. Positions 2-273.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04036.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni169 – 1702Substrate binding

Sequence similaritiesi

Belongs to the DapB family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0289.
HOGENOMiHOG000227153.
InParanoidiP04036.
KOiK00215.
OMAiHTVWFAD.
OrthoDBiEOG6SV5DS.
PhylomeDBiP04036.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00102. DapB.
InterProiIPR022663. DapB_C.
IPR000846. DapB_N.
IPR022664. DapB_N_CS.
IPR011770. Dihydrodipicolinate_Rdtase.
IPR023940. Dihydrodipicolinate_Rdtase_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.
TIGRFAMsiTIGR00036. dapB. 1 hit.
PROSITEiPS01298. DAPB. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P04036 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MHDANIRVAI AGAGGRMGRQ LIQAALALEG VQLGAALERE GSSLLGSDAG
60 70 80 90 100
ELAGAGKTGV TVQSSLDAVK DDFDVFIDFT RPEGTLNHLA FCRQHGKGMV
110 120 130 140 150
IGTTGFDEAG KQAIRDAAAD IAIVFAANFS VGVNVMLKLL EKAAKVMGDY
160 170 180 190 200
TDIEIIEAHH RHKVDAPSGT ALAMGEAIAH ALDKDLKDCA VYSREGHTGE
210 220 230 240 250
RVPGTIGFAT VRAGDIVGEH TAMFADIGER LEITHKASSR MTFANGAVRS
260 270
ALWLSGKESG LFDMRDVLDL NNL
Length:273
Mass (Da):28,757
Last modified:November 1, 1986 - v1
Checksum:i0ADE6837A6CF932C
GO

Mass spectrometryi

Molecular mass is 28758±8 Da from positions 1 - 273. Determined by ESI. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M10611 Genomic DNA. Translation: AAA23666.1.
U00096 Genomic DNA. Translation: AAC73142.1.
AP009048 Genomic DNA. Translation: BAB96600.1.
J01597 Genomic DNA. No translation available.
PIRiA00375. RDECPD.
RefSeqiNP_414572.1. NC_000913.3.
YP_488337.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73142; AAC73142; b0031.
BAB96600; BAB96600; BAB96600.
GeneIDi12932496.
944762.
KEGGiecj:Y75_p0031.
eco:b0031.
PATRICi32115153. VBIEscCol129921_0028.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M10611 Genomic DNA. Translation: AAA23666.1 .
U00096 Genomic DNA. Translation: AAC73142.1 .
AP009048 Genomic DNA. Translation: BAB96600.1 .
J01597 Genomic DNA. No translation available.
PIRi A00375. RDECPD.
RefSeqi NP_414572.1. NC_000913.3.
YP_488337.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1ARZ X-ray 2.60 A/B/C/D 1-273 [» ]
1DIH X-ray 2.20 A 1-273 [» ]
1DRU X-ray 2.20 A 1-273 [» ]
1DRV X-ray 2.20 A 1-273 [» ]
1DRW X-ray 2.20 A 1-273 [» ]
ProteinModelPortali P04036.
SMRi P04036. Positions 2-273.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-9399N.
IntActi P04036. 1 interaction.
STRINGi 511145.b0031.

Chemistry

BindingDBi P04036.

2D gel databases

SWISS-2DPAGE P04036.

Proteomic databases

PaxDbi P04036.
PRIDEi P04036.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC73142 ; AAC73142 ; b0031 .
BAB96600 ; BAB96600 ; BAB96600 .
GeneIDi 12932496.
944762.
KEGGi ecj:Y75_p0031.
eco:b0031.
PATRICi 32115153. VBIEscCol129921_0028.

Organism-specific databases

EchoBASEi EB0202.
EcoGenei EG10206. dapB.

Phylogenomic databases

eggNOGi COG0289.
HOGENOMi HOG000227153.
InParanoidi P04036.
KOi K00215.
OMAi HTVWFAD.
OrthoDBi EOG6SV5DS.
PhylomeDBi P04036.

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00018 .
BioCyci EcoCyc:DIHYDROPICRED-MONOMER.
ECOL316407:JW0029-MONOMER.
MetaCyc:DIHYDROPICRED-MONOMER.

Miscellaneous databases

EvolutionaryTracei P04036.
PROi P04036.

Gene expression databases

Genevestigatori P04036.

Family and domain databases

Gene3Di 3.40.50.720. 1 hit.
HAMAPi MF_00102. DapB.
InterProi IPR022663. DapB_C.
IPR000846. DapB_N.
IPR022664. DapB_N_CS.
IPR011770. Dihydrodipicolinate_Rdtase.
IPR023940. Dihydrodipicolinate_Rdtase_bac.
IPR016040. NAD(P)-bd_dom.
[Graphical view ]
PANTHERi PTHR20836. PTHR20836. 1 hit.
Pfami PF05173. DapB_C. 1 hit.
PF01113. DapB_N. 1 hit.
[Graphical view ]
PIRSFi PIRSF000161. DHPR. 1 hit.
TIGRFAMsi TIGR00036. dapB. 1 hit.
PROSITEi PS01298. DAPB. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Nucleotide sequence and expression of the Escherichia coli dapB gene."
    Bouvier J., Richaud C., Richaud F., Patte J.-C., Stragier P.
    J. Biol. Chem. 259:14829-14834(1984) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region."
    Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A.
    Nucleic Acids Res. 20:3305-3308(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Multiple regulatory signals in the control region of the Escherichia coli carAB operon."
    Bouvier J., Patte J.-C., Stragier P.
    Proc. Natl. Acad. Sci. U.S.A. 81:4139-4143(1984) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 269-273.
  6. "Expression, purification, and characterization of Escherichia coli dihydrodipicolinate reductase."
    Reddy S.G., Sacchettini J.C., Blanchard J.S.
    Biochemistry 34:3492-3501(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-18, FUNCTION, KINETIC PARAMETERS, SUBSTRATE SPECIFICITY, SUBUNIT, MASS SPECTROMETRY.
    Strain: K12.
  7. "Lysine represses transcription of the Escherichia coli dapB gene by preventing its activation by the ArgP activator."
    Bouvier J., Stragier P., Morales V., Remy E., Gutierrez C.
    J. Bacteriol. 190:5224-5229(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
    Strain: K12 / MG1655 / ATCC 47076.
  8. "NMR studies uncover alternate substrates for dihydrodipicolinate synthase and suggest that dihydrodipicolinate reductase is also a dehydratase."
    Devenish S.R., Blunt J.W., Gerrard J.A.
    J. Med. Chem. 53:4808-4812(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, IDENTIFICATION OF HTPA AS REACTION SUBSTRTATE, ACTIVE SITE.
  9. "Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase."
    Scapin G., Blanchard J.S., Sacchettini J.C.
    Biochemistry 34:3502-3512(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH NADPH.
    Strain: K12.
  10. "Interaction of pyridine nucleotide substrates with Escherichia coli dihydrodipicolinate reductase: thermodynamic and structural analysis of binary complexes."
    Reddy S.G., Scapin G., Blanchard J.S.
    Biochemistry 35:13294-13302(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH NAD OR NUCLEOTIDE SUBSTRATE ANALOGS.
    Strain: K12.
  11. "Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase in complex with NADH and the inhibitor 2,6-pyridinedicarboxylate."
    Scapin G., Reddy S.G., Zheng R., Blanchard J.S.
    Biochemistry 36:15081-15088(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEX WITH NAD AND A SUBSTRATE ANALOG INHIBITOR, ENZYME REGULATION, KINETIC PARAMETERS, REACTION MECHANISM, ACTIVE SITE, SITE, MUTAGENESIS OF HIS-159 AND LYS-163.
    Strain: K12.

Entry informationi

Entry nameiDAPB_ECOLI
AccessioniPrimary (citable) accession number: P04036
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1986
Last sequence update: November 1, 1986
Last modified: October 29, 2014
This is version 142 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 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 (PubMed:20503968).1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  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

External Data

Dasty 3