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Q088K8

- DAPF_SHEFN

UniProt

Q088K8 - DAPF_SHEFN

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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Shewanella frigidimarina (strain NCIMB 400)
Status
Reviewed - 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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei12 – 121SubstrateUniRule annotation
Binding sitei45 – 451SubstrateUniRule annotation
Binding sitei65 – 651SubstrateUniRule annotation
Active sitei74 – 741Proton donor/acceptorUniRule annotation
Binding sitei158 – 1581SubstrateUniRule annotation
Sitei160 – 1601Important for catalytic activityUniRule annotation
Binding sitei191 – 1911SubstrateUniRule annotation
Sitei209 – 2091Important for catalytic activityUniRule annotation
Active sitei218 – 2181Proton donor/acceptorUniRule annotation

GO - Molecular functioni

  1. diaminopimelate epimerase activity Source: UniProtKB-HAMAP

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

BioCyciSFRI318167:GIXS-467-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:Sfri_0445
OrganismiShewanella frigidimarina (strain NCIMB 400)
Taxonomic identifieri318167 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesShewanellaceaeShewanella
ProteomesiUP000000684: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

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 – 275275Diaminopimelate epimerasePRO_1000011963Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi74 ↔ 218

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi318167.Sfri_0445.

Structurei

3D structure databases

ProteinModelPortaliQ088K8.
SMRiQ088K8. Positions 2-275.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni9 – 102Substrate bindingUniRule annotation
Regioni74 – 763Substrate bindingUniRule annotation
Regioni209 – 2102Substrate bindingUniRule annotation
Regioni219 – 2202Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiLIVEPPY.
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.

Q088K8-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MIHFTKMHGL GNDFMVVDGV TQNVFFSPEQ IRRLADRNFG IGFDQLLLVE
60 70 80 90 100
PPYDPDLDFH YRIFNADGSE VEQCGNGARC FARFVRNKGL TQKNKIRVST
110 120 130 140 150
NSGKITLRIE RDGNVTVNMG VPVIEPSQIP FKAKKSEKTY LLQTPMQTYL
160 170 180 190 200
CGAISMGNPH CVIQVEDVQT VNVDEIGSSL TRHERFPKGV NVGFMQVINP
210 220 230 240 250
GHIKLRVYER GAAETLACGT GACAAAAVGQ LQDKLDKQVR VDLPGGSLII
260 270
NWEGEGKPLW MTGPAEHVYD GQIQL
Length:275
Mass (Da):30,448
Last modified:October 31, 2006 - v1
Checksum:i1C1AE7CBFD09ABBA
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000447 Genomic DNA. Translation: ABI70307.1.
RefSeqiYP_749145.1. NC_008345.1.

Genome annotation databases

EnsemblBacteriaiABI70307; ABI70307; Sfri_0445.
GeneIDi4278143.
KEGGisfr:Sfri_0445.
PATRICi23494671. VBISheFri14343_0461.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000447 Genomic DNA. Translation: ABI70307.1 .
RefSeqi YP_749145.1. NC_008345.1.

3D structure databases

ProteinModelPortali Q088K8.
SMRi Q088K8. Positions 2-275.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 318167.Sfri_0445.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABI70307 ; ABI70307 ; Sfri_0445 .
GeneIDi 4278143.
KEGGi sfr:Sfri_0445.
PATRICi 23494671. VBISheFri14343_0461.

Phylogenomic databases

eggNOGi COG0253.
HOGENOMi HOG000220466.
KOi K01778.
OMAi LIVEPPY.
OrthoDBi EOG6ND0M5.

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00025 .
BioCyci SFRI318167:GIXS-467-MONOMER.

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

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: NCIMB 400.

Entry informationi

Entry nameiDAPF_SHEFN
AccessioniPrimary (citable) accession number: Q088K8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: October 31, 2006
Last modified: October 29, 2014
This is version 56 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