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B0U6U5

- DAPF_XYLFM

UniProt

B0U6U5 - DAPF_XYLFM

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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Xylella fastidiosa (strain M12)
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 sitei20 – 201SubstrateUniRule annotation
Binding sitei53 – 531SubstrateUniRule annotation
Binding sitei73 – 731SubstrateUniRule annotation
Active sitei82 – 821Proton donor/acceptorUniRule annotation
Binding sitei167 – 1671SubstrateUniRule annotation
Sitei169 – 1691Important for catalytic activityUniRule annotation
Binding sitei200 – 2001SubstrateUniRule annotation
Sitei218 – 2181Important for catalytic activityUniRule annotation
Active sitei227 – 2271Proton 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

BioCyciXFAS405440:GH0D-851-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:Xfasm12_0823
OrganismiXylella fastidiosa (strain M12)
Taxonomic identifieri405440 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXylella
ProteomesiUP000008539: 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 – 284284Diaminopimelate epimerasePRO_1000099273Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi82 ↔ 227

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi405440.Xfasm12_0823.

Structurei

3D structure databases

ProteinModelPortaliB0U6U5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni82 – 843Substrate bindingUniRule annotation
Regioni218 – 2192Substrate 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.

B0U6U5-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MGVESVRCPL HFTKMQGAGN DFVVLDLRDG TPPPDAALVA WLADRHFGIG
60 70 80 90 100
CDQVIAIEPP RGVGVVAAYR IWNADGSAAQ QCGNGARCVA AWLVRDGSLA
110 120 130 140 150
DEHFLIDSPV QAHSVRCIGK DEYAVEMGLP VFEPERIPLS GFPNACAEYV
160 170 180 190 200
LSLQGEVLRC GAVSMGNPHA VVEVDLIDVA PVERIGPLLQ QHVAFPESVN
210 220 230 240 250
VGFVQVIDPG LVRLRVYERG AGETLACGSG ACAAAVVLMQ RGRVGRDVRV
260 270 280
VLPGGTLRVQ WPVSGGPVTL SGPARCVFDG VWYG
Length:284
Mass (Da):30,087
Last modified:April 8, 2008 - v1
Checksum:i3701D4D3CD478279
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000941 Genomic DNA. Translation: ACA11811.1.
RefSeqiYP_001775441.1. NC_010513.1.

Genome annotation databases

EnsemblBacteriaiACA11811; ACA11811; Xfasm12_0823.
GeneIDi6121385.
KEGGixfm:Xfasm12_0823.
PATRICi24138046. VBIXylFas124301_0980.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000941 Genomic DNA. Translation: ACA11811.1 .
RefSeqi YP_001775441.1. NC_010513.1.

3D structure databases

ProteinModelPortali B0U6U5.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 405440.Xfasm12_0823.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACA11811 ; ACA11811 ; Xfasm12_0823 .
GeneIDi 6121385.
KEGGi xfm:Xfasm12_0823.
PATRICi 24138046. VBIXylFas124301_0980.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00025 .
BioCyci XFAS405440:GH0D-851-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. "Whole genome sequences of two Xylella fastidiosa strains (M12 and M23) causing almond leaf scorch disease in California."
    Chen J., Xie G., Han S., Chertkov O., Sims D., Civerolo E.L.
    J. Bacteriol. 192:4534-4534(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: M12.

Entry informationi

Entry nameiDAPF_XYLFM
AccessioniPrimary (citable) accession number: B0U6U5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: April 8, 2008
Last modified: October 29, 2014
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

Documents

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

External Data

Dasty 3