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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Sphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256) (Sphingomonas alaskensis)
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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei13 – 131SubstrateUniRule annotation
Binding sitei46 – 461SubstrateUniRule annotation
Binding sitei64 – 641SubstrateUniRule annotation
Active sitei73 – 731Proton donor/acceptorUniRule annotation
Binding sitei148 – 1481SubstrateUniRule annotation
Sitei150 – 1501Important for catalytic activityUniRule annotation
Binding sitei181 – 1811SubstrateUniRule annotation
Sitei199 – 1991Important for catalytic activityUniRule annotation
Active sitei208 – 2081Proton 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

BioCyciSALA317655:GHHY-2770-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:Sala_2730
OrganismiSphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256) (Sphingomonas alaskensis)
Taxonomic identifieri317655 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeSphingopyxis
ProteomesiUP000006578 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 – 268268Diaminopimelate epimerasePRO_1000011972Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi73 ↔ 208

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi317655.Sala_2730.

Structurei

3D structure databases

ProteinModelPortaliQ1GPI7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni10 – 112Substrate bindingUniRule annotation
Regioni73 – 753Substrate bindingUniRule annotation
Regioni199 – 2002Substrate bindingUniRule annotation
Regioni209 – 2102Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
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.

Q1GPI7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MADRFTKMHG LGNDFVVIDA RVAPVEMTPA RAHAIADRRH GIGCDQLILL
60 70 80 90 100
EPSTSADVKM RIFNADGGEV EACGNATRCV ATLIGKPAVI ETLAGMLRVT
110 120 130 140 150
PADGGAEVTL GEPVFDWDHI PLAMPMDTRD MPVAWDELEH GAAVNVGNPH
160 170 180 190 200
IVFFVPEADA VALDQLGPRI ETDPLFPERV NVNVASLDGE NQLQLRVWER
210 220 230 240 250
GVGLTQACGT GACATAVAAI RAGLVRSPVT VALPGGDLVI RWAPGEPIVM
260
SGAATRVFDG ETDWAQFG
Length:268
Mass (Da):28,391
Last modified:June 27, 2006 - v1
Checksum:i6E8B6B31D8058712
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000356 Genomic DNA. Translation: ABF54435.1.
RefSeqiWP_011543000.1. NC_008048.1.
YP_617768.1. NC_008048.1.

Genome annotation databases

EnsemblBacteriaiABF54435; ABF54435; Sala_2730.
KEGGisal:Sala_2730.
PATRICi23694820. VBISphAla23391_2819.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000356 Genomic DNA. Translation: ABF54435.1.
RefSeqiWP_011543000.1. NC_008048.1.
YP_617768.1. NC_008048.1.

3D structure databases

ProteinModelPortaliQ1GPI7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi317655.Sala_2730.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABF54435; ABF54435; Sala_2730.
KEGGisal:Sala_2730.
PATRICi23694820. VBISphAla23391_2819.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciSALA317655:GHHY-2770-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 13593 / LMG 18877 / RB2256.

Entry informationi

Entry nameiDAPF_SPHAL
AccessioniPrimary (citable) accession number: Q1GPI7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: June 27, 2006
Last modified: April 29, 2015
This is version 65 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.