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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)
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: L-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 sitei13 – 131SubstrateUniRule annotation
Binding sitei47 – 471SubstrateUniRule annotation
Binding sitei65 – 651SubstrateUniRule annotation
Active sitei74 – 741Proton donor/acceptorUniRule annotation
Binding sitei149 – 1491SubstrateUniRule annotation
Sitei151 – 1511Important for catalytic activityUniRule annotation
Binding sitei182 – 1821SubstrateUniRule annotation
Sitei200 – 2001Important for catalytic activityUniRule annotation
Active sitei209 – 2091Proton 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

BioCyciSWIT392499:GHZK-2962-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:Swit_2928
OrganismiSphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)
Taxonomic identifieri392499 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeSphingomonas
ProteomesiUP000001989 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 – 274274Diaminopimelate epimerasePRO_1000011973Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi74 ↔ 209

Keywords - PTMi

Disulfide bond

Proteomic databases

PRIDEiA5VAG4.

Interactioni

Protein-protein interaction databases

STRINGi392499.Swit_2928.

Structurei

3D structure databases

ProteinModelPortaliA5VAG4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni10 – 112Substrate bindingUniRule annotation
Regioni74 – 763Substrate bindingUniRule annotation
Regioni200 – 2012Substrate bindingUniRule annotation
Regioni210 – 2112Substrate 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.

A5VAG4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQVRFHKMHG LGNDFVVIDA RATAPVEMTA ARARALADRK TGVGCDQLIL
60 70 80 90 100
LEPSAVADAR MRIFNADGSE VEACGNATRC VVSLLGGSAR IETVAGLLEG
110 120 130 140 150
RSADGQVSVE LGEPRFDWDA IPLAYAMDTR AMPVAWEELE APMAANVGNP
160 170 180 190 200
HVVFFVPETD AVALDRLGPR IETDPLFPAR INVNVATVDD RANIRLRVWE
210 220 230 240 250
RGVGLTDACG TGACATAVSA IRAGLVDSPV RVTLPGGPLT IDWAPGRPIV
260 270
MTGPATHVFT AETDLSAFGA DSRG
Length:274
Mass (Da):28,927
Last modified:July 10, 2007 - v1
Checksum:iBCCDAFE707FFEC04
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000699 Genomic DNA. Translation: ABQ69280.1.
RefSeqiWP_012049130.1. NC_009511.1.
YP_001263418.1. NC_009511.1.

Genome annotation databases

EnsemblBacteriaiABQ69280; ABQ69280; Swit_2928.
KEGGiswi:Swit_2928.
PATRICi23685041. VBISphWit55028_3464.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000699 Genomic DNA. Translation: ABQ69280.1.
RefSeqiWP_012049130.1. NC_009511.1.
YP_001263418.1. NC_009511.1.

3D structure databases

ProteinModelPortaliA5VAG4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi392499.Swit_2928.

Proteomic databases

PRIDEiA5VAG4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABQ69280; ABQ69280; Swit_2928.
KEGGiswi:Swit_2928.
PATRICi23685041. VBISphWit55028_3464.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciSWIT392499:GHZK-2962-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: RW1 / DSM 6014 / JCM 10273.

Entry informationi

Entry nameiDAPF_SPHWW
AccessioniPrimary (citable) accession number: A5VAG4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: July 10, 2007
Last modified: May 27, 2015
This is version 54 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.