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P0A6K1 (DAPF_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 86. 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:
Diaminopimelate epimerase

Short name=DAP epimerase
EC=5.1.1.7
Gene names
Name:dapF
Ordered Locus Names:b3809, JW5592
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length274 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. Only accepts DAP isomers with the L configuration. Ref.7 Ref.8 Ref.9

Catalytic activity

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate. Ref.7 Ref.9

Enzyme regulation

Inhibited by 2-(4-amino-4-carboxybutyl)aziri-dine-2-carboxylate (aziDAP) and iodoacetamide. Ref.7 Ref.9 Ref.10

Pathway

Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; DL-2,6-diaminopimelate from LL-2,6-diaminopimelate: step 1/1. HAMAP-Rule MF_00197

Subunit structure

Monomer. Ref.7

Subcellular location

Cytoplasm HAMAP-Rule MF_00197.

Sequence similarities

Belongs to the diaminopimelate epimerase family.

Biophysicochemical properties

Kinetic parameters:

KM=0.16 mM for D,L-DAP (at pH 7.8 and at 25 degrees Celsius) Ref.7 Ref.9

KM=0.26 mM for L,L-DAP (at pH 7.8 and at 25 degrees Celsius)

KM=0.36 mM for L,L-DAP (at pH 7.8 and at 25 degrees Celsius)

Sequence caution

The sequence AAA67605.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

The sequence CAA31413.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
   Biological processAmino-acid biosynthesis
Lysine biosynthesis
   Cellular componentCytoplasm
   Molecular functionIsomerase
   PTMDisulfide bond
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processlysine biosynthetic process via diaminopimelate

Inferred from electronic annotation. Source: UniProtKB-HAMAP

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functiondiaminopimelate epimerase activity

Inferred from direct assay PubMed 2689171. Source: EcoCyc

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 274274Diaminopimelate epimerase HAMAP-Rule MF_00197
PRO_0000149838

Regions

Region8 – 92Substrate By similarity
Region73 – 753Substrate binding By similarity
Region208 – 2092Substrate binding By similarity
Region218 – 2192Substrate binding By similarity

Sites

Active site731Proton donor/acceptor By similarity
Active site2171Proton donor/acceptor By similarity
Binding site111Substrate By similarity
Binding site441Substrate By similarity
Binding site641Substrate By similarity
Binding site1571Substrate By similarity
Binding site1901Substrate By similarity
Site1591Important for catalytic activity Potential
Site2081Important for catalytic activity Potential

Amino acid modifications

Disulfide bond73 ↔ 217 By similarity

Experimental info

Sequence conflict981S → T in CAA31413. Ref.1
Sequence conflict160 – 1612CV → WL in CAA31413. Ref.1
Sequence conflict200 – 2012EH → DD in CAA31413. Ref.1

Secondary structure

................................................... 274
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0A6K1 [UniParc].

Last modified March 29, 2005. Version 1.
Checksum: 4ACC137D2F5BD240

FASTA27430,209
        10         20         30         40         50         60 
MQFSKMHGLG NDFMVVDAVT QNVFFSPELI RRLADRHLGV GFDQLLVVEP PYDPELDFHY 

        70         80         90        100        110        120 
RIFNADGSEV AQCGNGARCF ARFVRLKGLT NKRDIRVSTA NGRMVLTVTD DDLVRVNMGE 

       130        140        150        160        170        180 
PNFEPSAVPF RANKAEKTYI MRAAEQTILC GVVSMGNPHC VIQVDDVDTA AVETLGPVLE 

       190        200        210        220        230        240 
SHERFPERAN IGFMQVVKRE HIRLRVYERG AGETQACGSG ACAAVAVGIQ QGLLAEEVRV 

       250        260        270 
ELPGGRLDIA WKGPGHPLYM TGPAVHVYDG FIHL 

« Hide

References

« Hide 'large scale' references
[1]"Nucleotide sequence of the dapF gene and flanking regions from Escherichia coli K12."
Richaud C., Printz C.
Nucleic Acids Res. 16:10367-10367(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[2]"Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes."
Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R.
Science 257:771-778(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[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]"Recombination at ColE1 cer requires the Escherichia coli xerC gene product, a member of the lambda integrase family of site-specific recombinases."
Colloms S.D., Sykora P., Szatmari G., Sherratt D.J.
J. Bacteriol. 172:6973-6980(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 259-274.
Strain: K12.
[6]"Comparative analysis of the cya locus in enterobacteria and related Gram-negative facultative anaerobes."
Trotot P., Sismeiro O., Vivares C., Glaser P., Bresson-Roy A., Danchin A.
Biochimie 78:277-287(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-8.
Strain: K12.
[7]"Purification and properties of diaminopimelic acid epimerase from Escherichia coli."
Wiseman J.S., Nichols J.S.
J. Biol. Chem. 259:8907-8914(1984) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
[8]"Molecular cloning, characterization, and chromosomal localization of dapF, the Escherichia coli gene for diaminopimelate epimerase."
Richaud C., Higgins W., Mengin-Lecreulx D., Stragier P.
J. Bacteriol. 169:1454-1459(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[9]"Analogs of diaminopimelic acid as inhibitors of meso-diaminopimelate dehydrogenase and LL-diaminopimelate epimerase."
Lam L.K., Arnold L.D., Kalantar T.H., Kelland J.G., Lane-Bell P.M., Palcic M.M., Pickard M.A., Vederas J.C.
J. Biol. Chem. 263:11814-11819(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
[10]"2-(4-Amino-4-carboxybutyl)aziridine-2-carboxylic acid. A potent irreversible inhibitor of diaminopimelic acid epimerase. Spontaneous formation from alpha-(halomethyl)diaminopimelic acids."
Gerhart F., Higgins W., Tardif C., Ducep J.B.
J. Med. Chem. 33:2157-2162(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: ENZYME REGULATION.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X12968 Genomic DNA. Translation: CAA31413.1. Different initiation.
M87049 Genomic DNA. Translation: AAA67605.1. Different initiation.
U00096 Genomic DNA. Translation: AAC76812.2.
AP009048 Genomic DNA. Translation: BAE77491.1.
M38257 Genomic DNA. Translation: AAA24761.1.
X66782 Genomic DNA. Translation: CAA47282.1.
PIRS01913. B65185.
RefSeqNP_418254.2. NC_000913.3.
YP_491632.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4IJZX-ray2.00A/B1-274[»]
4IK0X-ray2.05A/B1-274[»]
ProteinModelPortalP0A6K1.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-47856N.
IntActP0A6K1. 2 interactions.
STRING511145.b3809.

Proteomic databases

PaxDbP0A6K1.
PRIDEP0A6K1.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76812; AAC76812; b3809.
BAE77491; BAE77491; BAE77491.
GeneID12934260.
948364.
KEGGecj:Y75_p3368.
eco:b3809.
PATRIC32123119. VBIEscCol129921_3925.

Organism-specific databases

EchoBASEEB0205.
EcoGeneEG10209. dapF.

Phylogenomic databases

eggNOGCOG0253.
HOGENOMHOG000220466.
KOK01778.
OMALIVEPPY.
OrthoDBEOG6ND0M5.
PhylomeDBP0A6K1.

Enzyme and pathway databases

BioCycEcoCyc:DIAMINOPIMEPIM-MONOMER.
ECOL316407:JW5592-MONOMER.
MetaCyc:DIAMINOPIMEPIM-MONOMER.
UniPathwayUPA00034; UER00025.

Gene expression databases

GenevestigatorP0A6K1.

Family and domain databases

HAMAPMF_00197. DAP_epimerase.
InterProIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERPTHR31689. PTHR31689. 1 hit.
PfamPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsTIGR00652. DapF. 1 hit.
PROSITEPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

PROP0A6K1.

Entry information

Entry nameDAPF_ECOLI
AccessionPrimary (citable) accession number: P0A6K1
Secondary accession number(s): P08885 expand/collapse secondary AC list , P78126, Q2M8B5, Q8X8P8
Entry history
Integrated into UniProtKB/Swiss-Prot: March 29, 2005
Last sequence update: March 29, 2005
Last modified: June 11, 2014
This is version 86 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