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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Bacillus anthracis
Status
Reviewed-Annotation score: Annotation score: 3 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.By similarity

Catalytic activityi

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

Pathway:iL-lysine biosynthesis via DAP pathway

This protein is involved in step 1 of the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate.
Proteins known to be involved in this subpathway in this organism are:
  1. Diaminopimelate epimerase (dapF), Diaminopimelate epimerase (dapF)
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 DL-2,6-diaminopimelate from LL-2,6-diaminopimelate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei14 – 141SubstrateBy similarity
Binding sitei67 – 671SubstrateBy similarity
Active sitei76 – 761Proton donor/acceptorBy similarity
Binding sitei166 – 1661SubstrateBy similarity
Sitei168 – 1681Important for catalytic activitySequence Analysis
Binding sitei199 – 1991SubstrateBy similarity
Sitei217 – 2171Important for catalytic activitySequence Analysis
Active sitei226 – 2261Proton donor/acceptorBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciANTHRA:DAPF-MONOMER.
BANT260799:GJAJ-4884-MONOMER.
BANT261594:GJ7F-5046-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:BA_5170, GBAA_5170, BAS4806
OrganismiBacillus anthracis
Taxonomic identifieri1392 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillusBacillus cereus group
ProteomesiUP000000594 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 288288Diaminopimelate epimerasePRO_1000011837Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi76 ↔ 226By similarity

Keywords - PTMi

Disulfide bond

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

IntActiQ81XR2. 3 interactions.
STRINGi198094.BA_5170.

Structurei

Secondary structure

288
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi1 – 1111Combined sources
Beta strandi14 – 207Combined sources
Turni21 – 233Combined sources
Helixi28 – 303Combined sources
Helixi31 – 399Combined sources
Turni41 – 433Combined sources
Beta strandi48 – 547Combined sources
Beta strandi57 – 6711Combined sources
Turni76 – 794Combined sources
Helixi80 – 8910Combined sources
Beta strandi94 – 1029Combined sources
Beta strandi105 – 12622Combined sources
Helixi132 – 1343Combined sources
Beta strandi143 – 15210Combined sources
Beta strandi155 – 17218Combined sources
Helixi176 – 1783Combined sources
Turni181 – 1833Combined sources
Helixi184 – 1896Combined sources
Beta strandi199 – 2079Combined sources
Beta strandi210 – 2167Combined sources
Beta strandi218 – 2203Combined sources
Helixi227 – 23913Combined sources
Beta strandi249 – 2524Combined sources
Beta strandi257 – 2626Combined sources
Beta strandi268 – 2736Combined sources
Beta strandi275 – 28612Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2OTNX-ray2.40A/B1-288[»]
ProteinModelPortaliQ81XR2.
SMRiQ81XR2. Positions 1-287.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ81XR2.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni11 – 122SubstrateBy similarity
Regioni76 – 783Substrate bindingBy similarity
Regioni217 – 2182Substrate bindingBy similarity
Regioni227 – 2282Substrate bindingBy similarity

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.Curated

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMRIINSD.
OrthoDBiEOG6ND0M5.

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.

Q81XR2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSQFSFTKMH GLGNSYIYVN MFEEQIPEED LALVAEKVSN INTGIGADGM
60 70 80 90 100
ILICPSDVAP VKMRMFNNDG SEGKSCGNGL RCVAKYAYEH KLVEDTVFTI
110 120 130 140 150
ETLAGIVTAE VTVEEGKVTL AKIDMGAPRL TRAEIPMLGE GETPFIRENF
160 170 180 190 200
LYNNHRYAFT AVSMGNPHAV IFVDDVEQAP LTTLGPVLET HEMFPERVNV
210 220 230 240 250
EFIEILNEEE MNFRVWERGS GVTQACGTGA CAAVVASILN GKMERGKEIT
260 270 280
VHLAGGDLMI AWTEEGNVLM KGPAEVICRG VYEYKIEA
Length:288
Mass (Da):31,613
Last modified:June 1, 2003 - v1
Checksum:iF82364D2AC4202CA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016879 Genomic DNA. Translation: AAP28840.1.
AE017225 Genomic DNA. Translation: AAT57099.1.
AE017334 Genomic DNA. Translation: AAT70160.1.
RefSeqiNP_847354.1. NC_003997.3.
WP_000077386.1. NZ_KN050651.1.
YP_031049.1. NC_005945.1.

Genome annotation databases

EnsemblBacteriaiAAP28840; AAP28840; BA_5170.
AAT57099; AAT57099; BAS4806.
AAT70160; AAT70160; GBAA_5170.
GeneIDi1084119.
2848459.
KEGGiban:BA_5170.
bar:GBAA_5170.
bat:BAS4806.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016879 Genomic DNA. Translation: AAP28840.1.
AE017225 Genomic DNA. Translation: AAT57099.1.
AE017334 Genomic DNA. Translation: AAT70160.1.
RefSeqiNP_847354.1. NC_003997.3.
WP_000077386.1. NZ_KN050651.1.
YP_031049.1. NC_005945.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2OTNX-ray2.40A/B1-288[»]
ProteinModelPortaliQ81XR2.
SMRiQ81XR2. Positions 1-287.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ81XR2. 3 interactions.
STRINGi198094.BA_5170.

Protocols and materials databases

DNASUi1084119.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAP28840; AAP28840; BA_5170.
AAT57099; AAT57099; BAS4806.
AAT70160; AAT70160; GBAA_5170.
GeneIDi1084119.
2848459.
KEGGiban:BA_5170.
bar:GBAA_5170.
bat:BAS4806.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMRIINSD.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciANTHRA:DAPF-MONOMER.
BANT260799:GJAJ-4884-MONOMER.
BANT261594:GJ7F-5046-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ81XR2.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria."
    Read T.D., Peterson S.N., Tourasse N.J., Baillie L.W., Paulsen I.T., Nelson K.E., Tettelin H., Fouts D.E., Eisen J.A., Gill S.R., Holtzapple E.K., Okstad O.A., Helgason E., Rilstone J., Wu M., Kolonay J.F., Beanan M.J., Dodson R.J.
    , Brinkac L.M., Gwinn M.L., DeBoy R.T., Madpu R., Daugherty S.C., Durkin A.S., Haft D.H., Nelson W.C., Peterson J.D., Pop M., Khouri H.M., Radune D., Benton J.L., Mahamoud Y., Jiang L., Hance I.R., Weidman J.F., Berry K.J., Plaut R.D., Wolf A.M., Watkins K.L., Nierman W.C., Hazen A., Cline R.T., Redmond C., Thwaite J.E., White O., Salzberg S.L., Thomason B., Friedlander A.M., Koehler T.M., Hanna P.C., Kolstoe A.-B., Fraser C.M.
    Nature 423:81-86(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Ames / isolate Porton.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Ames ancestor.
  3. "Complete genome sequence of Bacillus anthracis Sterne."
    Brettin T.S., Bruce D., Challacombe J.F., Gilna P., Han C., Hill K., Hitchcock P., Jackson P., Keim P., Longmire J., Lucas S., Okinaka R., Richardson P., Rubin E., Tice H.
    Submitted (JAN-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Sterne.
  4. "Crystal structure of the catalytically active form of diamin epimerase from Bacillus anthracis."
    Matho M.H., Fukuda K., Santelli E., Jaroszewski L., Liddington R.C., Roper D.
    Submitted (FEB-2007) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.49 ANGSTROMS), SUBUNIT.

Entry informationi

Entry nameiDAPF_BACAN
AccessioniPrimary (citable) accession number: Q81XR2
Secondary accession number(s): Q6F086, Q6HRI9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: June 1, 2003
Last modified: July 22, 2015
This is version 94 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. 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

External Data

Dasty 3

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 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.