Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Xanthomonas axonopodis pv. citri (strain 306)
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 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

BioCyciXAXO190486:GH55-634-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:XAC0634
OrganismiXanthomonas axonopodis pv. citri (strain 306)
Taxonomic identifieri190486 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXanthomonas
ProteomesiUP000000576 Componenti: Chromosome

Subcellular locationi

  1. Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 284284Diaminopimelate epimerasePRO_0000149880Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi190486.XAC0634.

Structurei

3D structure databases

ProteinModelPortaliQ8PPQ1.
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.
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.

Q8PPQ1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSADGRSGRL RFTKMHGAGN DFVVLDLRDG TPPPDAALAA QLADRHFGIG
60 70 80 90 100
CDQILTIEAP RSEGAAAAYG IWNSDGSAAR QCGNGARCVA AWLVRDGTAQ
110 120 130 140 150
GERFIIDSPA TAHAVERLDG DRYAVAMGVP QFEPTQIPLA GFAHARDEYA
160 170 180 190 200
LPVHGETVRF GAVSMGNPHA VVEVGRVDAA PVERVGALLQ QNAAFPDSVN
210 220 230 240 250
VGFAQVVDPV HVRLRVFERG VGETLACGSG ACAAAAVLMQ RGRVERDVQV
260 270 280
SLPGGELRIR WPGDQEQVVM SGPAVFVFDG EWNR
Length:284
Mass (Da):30,092
Last modified:April 11, 2003 - v2
Checksum:i5E2FB26849BDE43C
GO

Sequence cautioni

The sequence AAM35523.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE008923 Genomic DNA. Translation: AAM35523.1. Different initiation.
RefSeqiNP_640987.1. NC_003919.1.

Genome annotation databases

EnsemblBacteriaiAAM35523; AAM35523; XAC0634.
KEGGixac:XAC0634.
PATRICi24053175. VBIXanAxo33670_0687.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE008923 Genomic DNA. Translation: AAM35523.1. Different initiation.
RefSeqiNP_640987.1. NC_003919.1.

3D structure databases

ProteinModelPortaliQ8PPQ1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi190486.XAC0634.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAM35523; AAM35523; XAC0634.
KEGGixac:XAC0634.
PATRICi24053175. VBIXanAxo33670_0687.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciXAXO190486:GH55-634-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. "Comparison of the genomes of two Xanthomonas pathogens with differing host specificities."
    da Silva A.C.R., Ferro J.A., Reinach F.C., Farah C.S., Furlan L.R., Quaggio R.B., Monteiro-Vitorello C.B., Van Sluys M.A., Almeida N.F. Jr., Alves L.M.C., do Amaral A.M., Bertolini M.C., Camargo L.E.A., Camarotte G., Cannavan F., Cardozo J., Chambergo F., Ciapina L.P.
    , Cicarelli R.M.B., Coutinho L.L., Cursino-Santos J.R., El-Dorry H., Faria J.B., Ferreira A.J.S., Ferreira R.C.C., Ferro M.I.T., Formighieri E.F., Franco M.C., Greggio C.C., Gruber A., Katsuyama A.M., Kishi L.T., Leite R.P., Lemos E.G.M., Lemos M.V.F., Locali E.C., Machado M.A., Madeira A.M.B.N., Martinez-Rossi N.M., Martins E.C., Meidanis J., Menck C.F.M., Miyaki C.Y., Moon D.H., Moreira L.M., Novo M.T.M., Okura V.K., Oliveira M.C., Oliveira V.R., Pereira H.A., Rossi A., Sena J.A.D., Silva C., de Souza R.F., Spinola L.A.F., Takita M.A., Tamura R.E., Teixeira E.C., Tezza R.I.D., Trindade dos Santos M., Truffi D., Tsai S.M., White F.F., Setubal J.C., Kitajima J.P.
    Nature 417:459-463(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 306.

Entry informationi

Entry nameiDAPF_XANAC
AccessioniPrimary (citable) accession number: Q8PPQ1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 25, 2002
Last sequence update: April 11, 2003
Last modified: April 1, 2015
This is version 78 of the entry and version 2 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

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.