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P04036 (DAPB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 139. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
4-hydroxy-tetrahydrodipicolinate reductase

Short name=HTPA reductase
EC=1.17.1.8
Gene names
Name:dapB
Ordered Locus Names:b0031, JW0029
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length273 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.6 Ref.8

Catalytic activity

(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)+ + H2O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H. Ref.8

Enzyme regulation

Is inhibited by 2,6-pyridine dicarboxylate (2,6-PDC or picolinate). Ref.11

Pathway

Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4. HAMAP-Rule MF_00102

Subunit structure

Homotetramer. Ref.6

Subcellular location

Cytoplasm HAMAP-Rule MF_00102.

Induction

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. Ref.7 Ref.11

Sequence similarities

Belongs to the DapB family.

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 (Ref.8).

Biophysicochemical properties

Kinetic parameters:

KM=1.6 µM for NADH Ref.6 Ref.11

KM=8 µM for NADPH

Mass spectrometry

Molecular mass is 28758±8 Da from positions 1 - 273. Determined by ESI. Ref.6

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 2732734-hydroxy-tetrahydrodipicolinate reductase HAMAP-Rule MF_00102
PRO_0000141437

Regions

Nucleotide binding12 – 176NAD(P) HAMAP-Rule MF_00102
Nucleotide binding102 – 1043NAD(P) HAMAP-Rule MF_00102
Nucleotide binding126 – 1294NAD(P) HAMAP-Rule MF_00102
Region169 – 1702Substrate binding HAMAP-Rule MF_00102

Sites

Active site1591Proton donor/acceptor Ref.8 Ref.11
Active site1631Proton donor Ref.8 Ref.11
Binding site381NAD
Binding site391NADP
Binding site1601Substrate

Experimental info

Mutagenesis1591H → A or Q: 135 to 200-fold reduction in catalytic activity. Ref.11
Mutagenesis1631K → A, C or Q: 625 to 830-fold reduction in catalytic activity. Ref.11

Secondary structure

................................................... 273
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P04036 [UniParc].

Last modified November 1, 1986. Version 1.
Checksum: 0ADE6837A6CF932C

FASTA27328,757
        10         20         30         40         50         60 
MHDANIRVAI AGAGGRMGRQ LIQAALALEG VQLGAALERE GSSLLGSDAG ELAGAGKTGV 

        70         80         90        100        110        120 
TVQSSLDAVK DDFDVFIDFT RPEGTLNHLA FCRQHGKGMV IGTTGFDEAG KQAIRDAAAD 

       130        140        150        160        170        180 
IAIVFAANFS VGVNVMLKLL EKAAKVMGDY TDIEIIEAHH RHKVDAPSGT ALAMGEAIAH 

       190        200        210        220        230        240 
ALDKDLKDCA VYSREGHTGE RVPGTIGFAT VRAGDIVGEH TAMFADIGER LEITHKASSR 

       250        260        270 
MTFANGAVRS ALWLSGKESG LFDMRDVLDL NNL 

« Hide

References

« Hide 'large scale' references
[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]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M10611 Genomic DNA. Translation: AAA23666.1.
U00096 Genomic DNA. Translation: AAC73142.1.
AP009048 Genomic DNA. Translation: BAB96600.1.
J01597 Genomic DNA. No translation available.
PIRRDECPD. A00375.
RefSeqNP_414572.1. NC_000913.3.
YP_488337.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalP04036.
SMRP04036. Positions 2-273.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-9399N.
IntActP04036. 1 interaction.
STRING511145.b0031.

Chemistry

BindingDBP04036.

2D gel databases

SWISS-2DPAGEP04036.

Proteomic databases

PaxDbP04036.
PRIDEP04036.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC73142; AAC73142; b0031.
BAB96600; BAB96600; BAB96600.
GeneID12932496.
944762.
KEGGecj:Y75_p0031.
eco:b0031.
PATRIC32115153. VBIEscCol129921_0028.

Organism-specific databases

EchoBASEEB0202.
EcoGeneEG10206. dapB.

Phylogenomic databases

eggNOGCOG0289.
HOGENOMHOG000227153.
KOK00215.
OMAIVMAPNM.
OrthoDBEOG6SV5DS.
PhylomeDBP04036.
ProtClustDBPRK00048.

Enzyme and pathway databases

BioCycEcoCyc:DIHYDROPICRED-MONOMER.
ECOL316407:JW0029-MONOMER.
MetaCyc:DIHYDROPICRED-MONOMER.
UniPathwayUPA00034; UER00018.

Gene expression databases

GenevestigatorP04036.

Family and domain databases

Gene3D3.40.50.720. 1 hit.
HAMAPMF_00102. DapB.
InterProIPR022663. DapB_C.
IPR000846. DapB_N.
IPR022664. DapB_N_CS.
IPR011770. Dihydrodipicolinate_Rdtase.
IPR023940. Dihydrodipicolinate_Rdtase_bac.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PANTHERPTHR20836. PTHR20836. 1 hit.
PfamPF05173. DapB_C. 1 hit.
PF01113. DapB_N. 1 hit.
[Graphical view]
PIRSFPIRSF000161. DHPR. 1 hit.
TIGRFAMsTIGR00036. dapB. 1 hit.
PROSITEPS01298. DAPB. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP04036.
PROP04036.

Entry information

Entry nameDAPB_ECOLI
AccessionPrimary (citable) accession number: P04036
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1986
Last sequence update: November 1, 1986
Last modified: April 16, 2014
This is version 139 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

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