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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Beijerinckia indica subsp. indica (strain ATCC 9039 / DSM 1715 / NCIB 8712)
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.UniRule annotation

Catalytic activityi

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

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.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. 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 sitei17 – 171SubstrateUniRule annotation
Binding sitei49 – 491SubstrateUniRule annotation
Binding sitei69 – 691SubstrateUniRule annotation
Active sitei78 – 781Proton donor/acceptorUniRule annotation
Binding sitei172 – 1721SubstrateUniRule annotation
Sitei174 – 1741Important for catalytic activityUniRule annotation
Binding sitei205 – 2051SubstrateUniRule annotation
Sitei223 – 2231Important for catalytic activityUniRule annotation
Active sitei232 – 2321Proton donor/acceptorUniRule annotation

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

BioCyciBIND395963:GJA7-3460-MONOMER.
UniPathwayiUPA00034; UER00025.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimeraseUniRule annotation (EC:5.1.1.7UniRule annotation)
Short name:
DAP epimeraseUniRule annotation
Gene namesi
Name:dapFUniRule annotation
Ordered Locus Names:Bind_3404
OrganismiBeijerinckia indica subsp. indica (strain ATCC 9039 / DSM 1715 / NCIB 8712)
Taxonomic identifieri395963 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBeijerinckiaceaeBeijerinckia
ProteomesiUP000001695 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 297297Diaminopimelate epimerasePRO_1000099220Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi78 ↔ 232

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi395963.Bind_3404.

Structurei

3D structure databases

ProteinModelPortaliB2IEM1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni14 – 152Substrate bindingUniRule annotation
Regioni78 – 803Substrate bindingUniRule annotation
Regioni223 – 2242Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMTTRTWE.
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.

B2IEM1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSALANRFVT KMNGLGNAIV VLDLRGTGIV ISAAEARAIG QGKGLHFDQL
60 70 80 90 100
MVLHDPLSPG SAAFMRIYNI DGSLAGACGN GTRCVAWTLL REDHRIGAEL
110 120 130 140 150
MLETAAGQLA CLKLAEDRFS VDMGKPAFAW DAIPLAHPVP DTNAVDLARD
160 170 180 190 200
LAVLPPVDPD ALRKASMVNM GNPHAVLFVA DQDACDLALV GPVLEHHPLF
210 220 230 240 250
PDRANISIAT VVSPDHIVLK VWERGAGATL ACGSAACATL VAAVRHGLAA
260 270 280 290
REARISLPGG DLTIAWRAAD DHVIMTGPVT FEFTTRLDPS LFQALVA
Length:297
Mass (Da):31,270
Last modified:June 10, 2008 - v1
Checksum:iE8B04CA4162E5F10
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001016 Genomic DNA. Translation: ACB96961.1.
RefSeqiWP_012386309.1. NC_010581.1.

Genome annotation databases

EnsemblBacteriaiACB96961; ACB96961; Bind_3404.
KEGGibid:Bind_3404.
PATRICi21089907. VBIBeiInd21058_3860.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001016 Genomic DNA. Translation: ACB96961.1.
RefSeqiWP_012386309.1. NC_010581.1.

3D structure databases

ProteinModelPortaliB2IEM1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi395963.Bind_3404.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACB96961; ACB96961; Bind_3404.
KEGGibid:Bind_3404.
PATRICi21089907. VBIBeiInd21058_3860.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMTTRTWE.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciBIND395963:GJA7-3460-MONOMER.

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

  1. "Complete sequence of chromosome of Beijerinckia indica subsp. indica ATCC 9039."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., LaButti K., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Dunfield P.F., Dedysh S.N.
    , Liesack W., Saw J.H., Alam M., Chen Y., Murrell J.C., Richardson P.
    Submitted (MAR-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 9039 / DSM 1715 / NCIB 8712.

Entry informationi

Entry nameiDAPF_BEII9
AccessioniPrimary (citable) accession number: B2IEM1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: June 10, 2008
Last modified: July 22, 2015
This is version 50 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

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.