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P0A6K1

- DAPF_ECOLI

UniProt

P0A6K1 - DAPF_ECOLI

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Protein

Diaminopimelate epimerase

Gene

dapF

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

Functioni

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.3 Publications

Catalytic activityi

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.2 Publications

Enzyme regulationi

Inhibited by 2-(4-amino-4-carboxybutyl)aziri-dine-2-carboxylate (aziDAP) and iodoacetamide.3 Publications

Kineticsi

  1. KM=0.16 mM for D,L-DAP (at pH 7.8 and at 25 degrees Celsius)2 Publications
  2. KM=0.26 mM for L,L-DAP (at pH 7.8 and at 25 degrees Celsius)2 Publications
  3. KM=0.36 mM for L,L-DAP (at pH 7.8 and at 25 degrees Celsius)2 Publications

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei11 – 111SubstrateBy similarity
Binding sitei44 – 441SubstrateBy similarity
Binding sitei64 – 641SubstrateBy similarity
Active sitei73 – 731Proton donor/acceptorBy similarity
Binding sitei157 – 1571SubstrateBy similarity
Sitei159 – 1591Important for catalytic activitySequence Analysis
Binding sitei190 – 1901SubstrateBy similarity
Sitei208 – 2081Important for catalytic activitySequence Analysis
Active sitei217 – 2171Proton donor/acceptorBy similarity

GO - Molecular functioni

  1. diaminopimelate epimerase activity Source: EcoCyc

GO - Biological processi

  1. lysine biosynthetic process via diaminopimelate Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciEcoCyc:DIAMINOPIMEPIM-MONOMER.
ECOL316407:JW5592-MONOMER.
MetaCyc:DIAMINOPIMEPIM-MONOMER.
UniPathwayiUPA00034; UER00025.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimerase (EC:5.1.1.7)
Short name:
DAP epimerase
Gene namesi
Name:dapF
Ordered Locus Names:b3809, JW5592
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10209. dapF.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 274274Diaminopimelate epimerasePRO_0000149838Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi73 ↔ 217By similarity

Keywords - PTMi

Disulfide bond

Proteomic databases

PaxDbiP0A6K1.
PRIDEiP0A6K1.

Expressioni

Gene expression databases

GenevestigatoriP0A6K1.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

DIPiDIP-47856N.
IntActiP0A6K1. 2 interactions.
STRINGi511145.b3809.

Structurei

Secondary structure

1
274
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 87Combined sources
Beta strandi11 – 177Combined sources
Beta strandi19 – 213Combined sources
Helixi27 – 348Combined sources
Turni36 – 383Combined sources
Beta strandi43 – 497Combined sources
Beta strandi57 – 648Combined sources
Beta strandi69 – 713Combined sources
Helixi74 – 8613Combined sources
Beta strandi93 – 997Combined sources
Beta strandi102 – 1087Combined sources
Beta strandi114 – 1174Combined sources
Helixi125 – 1273Combined sources
Beta strandi137 – 1437Combined sources
Beta strandi146 – 16520Combined sources
Helixi167 – 1693Combined sources
Helixi172 – 1809Combined sources
Beta strandi190 – 1989Combined sources
Beta strandi201 – 2088Combined sources
Turni209 – 2113Combined sources
Beta strandi212 – 2154Combined sources
Helixi218 – 23013Combined sources
Beta strandi236 – 2427Combined sources
Beta strandi245 – 2517Combined sources
Beta strandi258 – 2625Combined sources
Beta strandi265 – 2728Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4IJZX-ray2.00A/B1-274[»]
4IK0X-ray2.05A/B1-274[»]
ProteinModelPortaliP0A6K1.
SMRiP0A6K1. Positions 1-274.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni8 – 92SubstrateBy similarity
Regioni73 – 753Substrate bindingBy similarity
Regioni208 – 2092Substrate bindingBy similarity
Regioni218 – 2192Substrate bindingBy similarity

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.Curated

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
InParanoidiP0A6K1.
KOiK01778.
OMAiLIVEPPY.
OrthoDBiEOG6ND0M5.
PhylomeDBiP0A6K1.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0A6K1-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MQFSKMHGLG NDFMVVDAVT QNVFFSPELI RRLADRHLGV GFDQLLVVEP
60 70 80 90 100
PYDPELDFHY RIFNADGSEV AQCGNGARCF ARFVRLKGLT NKRDIRVSTA
110 120 130 140 150
NGRMVLTVTD DDLVRVNMGE PNFEPSAVPF RANKAEKTYI MRAAEQTILC
160 170 180 190 200
GVVSMGNPHC VIQVDDVDTA AVETLGPVLE SHERFPERAN IGFMQVVKRE
210 220 230 240 250
HIRLRVYERG AGETQACGSG ACAAVAVGIQ QGLLAEEVRV ELPGGRLDIA
260 270
WKGPGHPLYM TGPAVHVYDG FIHL
Length:274
Mass (Da):30,209
Last modified:March 29, 2005 - v1
Checksum:i4ACC137D2F5BD240
GO

Sequence cautioni

The sequence AAA67605.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence CAA31413.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti98 – 981S → T in CAA31413. (PubMed:3057443)Curated
Sequence conflicti160 – 1612CV → WL in CAA31413. (PubMed:3057443)Curated
Sequence conflicti200 – 2012EH → DD in CAA31413. (PubMed:3057443)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiB65185. S01913.
RefSeqiNP_418254.2. NC_000913.3.
YP_491632.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC76812; AAC76812; b3809.
BAE77491; BAE77491; BAE77491.
GeneIDi12934260.
948364.
KEGGiecj:Y75_p3368.
eco:b3809.
PATRICi32123119. VBIEscCol129921_3925.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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 .
PIRi B65185. S01913.
RefSeqi NP_418254.2. NC_000913.3.
YP_491632.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4IJZ X-ray 2.00 A/B 1-274 [» ]
4IK0 X-ray 2.05 A/B 1-274 [» ]
ProteinModelPortali P0A6K1.
SMRi P0A6K1. Positions 1-274.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-47856N.
IntActi P0A6K1. 2 interactions.
STRINGi 511145.b3809.

Proteomic databases

PaxDbi P0A6K1.
PRIDEi P0A6K1.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC76812 ; AAC76812 ; b3809 .
BAE77491 ; BAE77491 ; BAE77491 .
GeneIDi 12934260.
948364.
KEGGi ecj:Y75_p3368.
eco:b3809.
PATRICi 32123119. VBIEscCol129921_3925.

Organism-specific databases

EchoBASEi EB0205.
EcoGenei EG10209. dapF.

Phylogenomic databases

eggNOGi COG0253.
HOGENOMi HOG000220466.
InParanoidi P0A6K1.
KOi K01778.
OMAi LIVEPPY.
OrthoDBi EOG6ND0M5.
PhylomeDBi P0A6K1.

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00025 .
BioCyci EcoCyc:DIAMINOPIMEPIM-MONOMER.
ECOL316407:JW5592-MONOMER.
MetaCyc:DIAMINOPIMEPIM-MONOMER.

Miscellaneous databases

PROi P0A6K1.

Gene expression databases

Genevestigatori P0A6K1.

Family and domain databases

HAMAPi MF_00197. DAP_epimerase.
InterProi IPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view ]
PANTHERi PTHR31689. PTHR31689. 1 hit.
Pfami PF01678. DAP_epimerase. 2 hits.
[Graphical view ]
TIGRFAMsi TIGR00652. DapF. 1 hit.
PROSITEi PS01326. DAP_EPIMERASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. 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.

Entry informationi

Entry nameiDAPF_ECOLI
AccessioniPrimary (citable) accession number: P0A6K1
Secondary accession number(s): P08885
, P78126, Q2M8B5, Q8X8P8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 29, 2005
Last sequence update: March 29, 2005
Last modified: November 26, 2014
This is version 89 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, 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