Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

Q9PD98 (DAPF_XYLFA) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 72. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Diaminopimelate epimerase

Short name=DAP epimerase
EC=5.1.1.7
Gene names
Name:dapF
Ordered Locus Names:XF_1481
OrganismXylella fastidiosa (strain 9a5c) [Complete proteome] [HAMAP]
Taxonomic identifier160492 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXylella

Protein attributes

Sequence length284 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 By similarity. HAMAP-Rule MF_00197

Catalytic activity

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate. HAMAP-Rule MF_00197

Pathway

Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; DL-2,6-diaminopimelate from LL-2,6-diaminopimelate: step 1/1. HAMAP-Rule MF_00197

Subcellular location

Cytoplasm By similarity HAMAP-Rule MF_00197.

Sequence similarities

Belongs to the diaminopimelate epimerase family.

Ontologies

Keywords
   Biological processAmino-acid biosynthesis
Lysine biosynthesis
   Cellular componentCytoplasm
   Molecular functionIsomerase
   PTMDisulfide bond
   Technical termComplete proteome
Gene Ontology (GO)
   Biological_processlysine biosynthetic process via diaminopimelate

Inferred from electronic annotation. Source: UniProtKB-HAMAP

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functiondiaminopimelate epimerase activity

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 284284Diaminopimelate epimerase HAMAP-Rule MF_00197
PRO_0000149882

Regions

Region82 – 843Substrate binding By similarity
Region218 – 2192Substrate binding By similarity

Sites

Active site821Proton donor/acceptor By similarity
Active site2271Proton donor/acceptor By similarity
Binding site201Substrate By similarity
Binding site531Substrate By similarity
Binding site731Substrate By similarity
Binding site1671Substrate By similarity
Binding site2001Substrate By similarity
Site1691Important for catalytic activity By similarity
Site2181Important for catalytic activity By similarity

Amino acid modifications

Disulfide bond82 ↔ 227 HAMAP-Rule MF_00197

Sequences

Sequence LengthMass (Da)Tools
Q9PD98 [UniParc].

Last modified October 1, 2000. Version 1.
Checksum: AFB170A1E437D918

FASTA28430,123
        10         20         30         40         50         60 
MGVESVRCPL HFTKMQGAGN DFVVLDLRDG TPPPDVALVA WLADRHFGIG CDQVIAIEPP 

        70         80         90        100        110        120 
RGVGVFAAYR IWNADGSAAQ QCGNGARCVA AWLVRDGSVA DEHFLIDSPV QAHLVRCIGK 

       130        140        150        160        170        180 
DEYAVEMGLP VFEPERIPLS GFPNACGEYV LSLQGEVLRC GAVSMGNPHA VVEVDLIDVA 

       190        200        210        220        230        240 
PVERIGSLLQ QHVAFPESVN VGFVQVIDPG LVRLRVYERG AGETLACGSG ACAAAVVLMQ 

       250        260        270        280 
RGRVGRDVRV VLPGGTLRVQ WPVSGGPVTL SGPAKCVFDG VWYG 

« Hide

References

[1]"The genome sequence of the plant pathogen Xylella fastidiosa."
Simpson A.J.G., Reinach F.C., Arruda P., Abreu F.A., Acencio M., Alvarenga R., Alves L.M.C., Araya J.E., Baia G.S., Baptista C.S., Barros M.H., Bonaccorsi E.D., Bordin S., Bove J.M., Briones M.R.S., Bueno M.R.P., Camargo A.A., Camargo L.E.A. expand/collapse author list , Carraro D.M., Carrer H., Colauto N.B., Colombo C., Costa F.F., Costa M.C.R., Costa-Neto C.M., Coutinho L.L., Cristofani M., Dias-Neto E., Docena C., El-Dorry H., Facincani A.P., Ferreira A.J.S., Ferreira V.C.A., Ferro J.A., Fraga J.S., Franca S.C., Franco M.C., Frohme M., Furlan L.R., Garnier M., Goldman G.H., Goldman M.H.S., Gomes S.L., Gruber A., Ho P.L., Hoheisel J.D., Junqueira M.L., Kemper E.L., Kitajima J.P., Krieger J.E., Kuramae E.E., Laigret F., Lambais M.R., Leite L.C.C., Lemos E.G.M., Lemos M.V.F., Lopes S.A., Lopes C.R., Machado J.A., Machado M.A., Madeira A.M.B.N., Madeira H.M.F., Marino C.L., Marques M.V., Martins E.A.L., Martins E.M.F., Matsukuma A.Y., Menck C.F.M., Miracca E.C., Miyaki C.Y., Monteiro-Vitorello C.B., Moon D.H., Nagai M.A., Nascimento A.L.T.O., Netto L.E.S., Nhani A. Jr., Nobrega F.G., Nunes L.R., Oliveira M.A., de Oliveira M.C., de Oliveira R.C., Palmieri D.A., Paris A., Peixoto B.R., Pereira G.A.G., Pereira H.A. Jr., Pesquero J.B., Quaggio R.B., Roberto P.G., Rodrigues V., de Rosa A.J.M., de Rosa V.E. Jr., de Sa R.G., Santelli R.V., Sawasaki H.E., da Silva A.C.R., da Silva A.M., da Silva F.R., Silva W.A. Jr., da Silveira J.F., Silvestri M.L.Z., Siqueira W.J., de Souza A.A., de Souza A.P., Terenzi M.F., Truffi D., Tsai S.M., Tsuhako M.H., Vallada H., Van Sluys M.A., Verjovski-Almeida S., Vettore A.L., Zago M.A., Zatz M., Meidanis J., Setubal J.C.
Nature 406:151-159(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: 9a5c.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE003849 Genomic DNA. Translation: AAF84290.1.
PIRD82677.
RefSeqNP_298770.1. NC_002488.3.

3D structure databases

ProteinModelPortalQ9PD98.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING160492.XF1481.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAF84290; AAF84290; XF_1481.
GeneID1127027.
KEGGxfa:XF1481.
PATRIC24133068. VBIXylFas578_1562.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0253.
KOK01778.
OMACFARFVL.
OrthoDBEOG6ND0M5.
ProtClustDBPRK00450.

Enzyme and pathway databases

UniPathwayUPA00034; UER00025.

Family and domain databases

HAMAPMF_00197. DAP_epimerase.
InterProIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERPTHR31689:SF0. PTHR31689:SF0. 1 hit.
PfamPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsTIGR00652. DapF. 1 hit.
PROSITEPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameDAPF_XYLFA
AccessionPrimary (citable) accession number: Q9PD98
Entry history
Integrated into UniProtKB/Swiss-Prot: June 6, 2002
Last sequence update: October 1, 2000
Last modified: February 19, 2014
This is version 72 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways