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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Xanthomonas campestris pv. campestris (strain 8004)
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: 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)DescriptionActionsGraphical viewLength
Binding sitei20SubstrateUniRule annotation1
Binding sitei53SubstrateUniRule annotation1
Binding sitei73SubstrateUniRule annotation1
Active sitei82Proton donor/acceptorUniRule annotation1
Binding sitei167SubstrateUniRule annotation1
Sitei169Important for catalytic activityUniRule annotation1
Binding sitei200SubstrateUniRule annotation1
Sitei218Important for catalytic activityUniRule annotation1
Active sitei227Proton donor/acceptorUniRule annotation1

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

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:XC_0662
OrganismiXanthomonas campestris pv. campestris (strain 8004)
Taxonomic identifieri314565 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXanthomonas
Proteomesi
  • UP000000420 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000119841 – 284Diaminopimelate epimeraseAdd BLAST284

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi82 ↔ 227

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi314565.XC_0662.

Structurei

3D structure databases

ProteinModelPortaliQ4UYY2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni82 – 84Substrate bindingUniRule annotation3
Regioni218 – 219Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiRFTKMQG.
OrthoDBiPOG091H01QC.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
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.

Q4UYY2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSADVHTGRL RFTKMHGAGN DFVVLDLRNG TPPPDASLAA RLADRHFGVG
60 70 80 90 100
CDQILTIETP RSAEAVAAYR IWNSDGSHSQ QCGNGARCVA AWLVREGTAQ
110 120 130 140 150
GDVFTIDSPF TAHRVERLDA GTYSVAMGVP QFEPTQIPLA GFAHARDEYA
160 170 180 190 200
LPVHGETVRF GAVSMGNPHA VVEVGRVDAA PVERVGALLQ QNAAFPESVN
210 220 230 240 250
VGFAQVVDPA HVRLRVYERG VGETLACGSG ACAAAVVLMH RGRVERDVRV
260 270 280
SLPGGELRIR WAGEQAQVVM SGPAVFVFDG EWNQ
Length:284
Mass (Da):30,361
Last modified:July 5, 2005 - v1
Checksum:i281E3B5AC0B1DEBD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000050 Genomic DNA. Translation: AAY47741.1.
RefSeqiWP_011038591.1. NC_007086.1.

Genome annotation databases

EnsemblBacteriaiAAY47741; AAY47741; XC_0662.
KEGGixcb:XC_0662.
PATRICi24062610. VBIXanCam24967_0715.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000050 Genomic DNA. Translation: AAY47741.1.
RefSeqiWP_011038591.1. NC_007086.1.

3D structure databases

ProteinModelPortaliQ4UYY2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi314565.XC_0662.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAY47741; AAY47741; XC_0662.
KEGGixcb:XC_0662.
PATRICi24062610. VBIXanCam24967_0715.

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiRFTKMQG.
OrthoDBiPOG091H01QC.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
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...

Entry informationi

Entry nameiDAPF_XANC8
AccessioniPrimary (citable) accession number: Q4UYY2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: July 5, 2005
Last modified: November 2, 2016
This is version 66 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

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

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 one 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.