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

Succinyl-diaminopimelate desuccinylase

Gene

dapE

Organism
Xylella fastidiosa (strain Temecula1 / ATCC 700964)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP), forming succinate and LL-2,6-diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls.UniRule annotation

Catalytic activityi

N-succinyl-LL-2,6-diaminoheptanedioate + H2O = succinate + LL-2,6-diaminoheptanedioate.UniRule annotation

Cofactori

Protein has several cofactor binding sites:
  • Zn2+UniRule annotationNote: Binds 1 Zn2+ ion per subunit.UniRule annotation
  • Co2+UniRule annotationNote: Binds 1 Co2+ ion per subunit.UniRule annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi66 – 661Cobalt or zinc 1UniRule annotation
Active sitei68 – 681UniRule annotation
Metal bindingi99 – 991Cobalt or zinc 1UniRule annotation
Metal bindingi99 – 991Cobalt or zinc 2UniRule annotation
Active sitei133 – 1331Proton acceptorUniRule annotation
Metal bindingi134 – 1341Cobalt or zinc 2UniRule annotation
Metal bindingi162 – 1621Cobalt or zinc 1UniRule annotation
Metal bindingi348 – 3481Cobalt or zinc 2UniRule annotation

GO - Molecular functioni

  1. cobalt ion binding Source: UniProtKB-HAMAP
  2. metallopeptidase activity Source: InterPro
  3. succinyl-diaminopimelate desuccinylase activity Source: UniProtKB-HAMAP
  4. zinc ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. diaminopimelate biosynthetic process Source: UniProtKB-HAMAP
  2. lysine biosynthetic process via diaminopimelate Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Amino-acid biosynthesis, Diaminopimelate biosynthesis, Lysine biosynthesis

Keywords - Ligandi

Cobalt, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciXFAS183190:GIX4-88-MONOMER.
UniPathwayiUPA00034; UER00021.

Protein family/group databases

MEROPSiM20.010.

Names & Taxonomyi

Protein namesi
Recommended name:
Succinyl-diaminopimelate desuccinylaseUniRule annotation (EC:3.5.1.18UniRule annotation)
Short name:
SDAP desuccinylaseUniRule annotation
Alternative name(s):
N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolaseUniRule annotation
Gene namesi
Name:dapEUniRule annotation
Ordered Locus Names:PD_0088
OrganismiXylella fastidiosa (strain Temecula1 / ATCC 700964)
Taxonomic identifieri183190 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXylella
ProteomesiUP000002516: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 377377Succinyl-diaminopimelate desuccinylasePRO_0000375792Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi183190.PD0088.

Structurei

3D structure databases

ProteinModelPortaliQ87F49.
SMRiQ87F49. Positions 2-374.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase M20A family. DapE subfamily.UniRule annotation

Phylogenomic databases

eggNOGiCOG0624.
KOiK01439.
OMAiAGFACEH.
OrthoDBiEOG60651W.

Family and domain databases

Gene3Di3.30.70.360. 1 hit.
HAMAPiMF_01690. DapE.
InterProiIPR001261. ArgE/DapE_CS.
IPR005941. DapE_proteobac.
IPR002933. Peptidase_M20.
IPR011650. Peptidase_M20_dimer.
[Graphical view]
PfamiPF07687. M20_dimer. 1 hit.
PF01546. Peptidase_M20. 1 hit.
[Graphical view]
SUPFAMiSSF55031. SSF55031. 1 hit.
TIGRFAMsiTIGR01246. dapE_proteo. 1 hit.
PROSITEiPS00759. ARGE_DAPE_CPG2_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q87F49-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDVLDLACD LISRPSMTPD DAGCQEMIAK RLERAGFICE HLRYAAVSNL
60 70 80 90 100
WATHGRGAPV LVLLGHTDVV PPGPVEAWTS DPFMPDMRNG ILYGRGAADM
110 120 130 140 150
KGSVAAFVIA AERFLAAYPQ HPGTLAILLT SDEEGQAIDG VRKVAETLRQ
160 170 180 190 200
RGQGIDWCLT GEPSSSKRLG DLLRVGRRGS LSATLHVKGV QGHVAYPHQA
210 220 230 240 250
RNPIHLALPA FAALTARHWD DGYESFPSTS LQISNIHAGT GANNVIPGAL
260 270 280 290 300
EVAFNLRYNP HWIAPRLESE IVALLDQHGL DYTLHWHRSG EPFYTPEGKL
310 320 330 340 350
RRIAREVLER FSGAPPEEST GGGTSDARFI APLGAQCIEV GPVNASIHQV
360 370
DEHVCLSDLE ALPDLYQLLI ERLLAEH
Length:377
Mass (Da):40,992
Last modified:June 1, 2003 - v1
Checksum:i7269AD1D6B67C98F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009442 Genomic DNA. Translation: AAO27988.1.
RefSeqiNP_778339.1. NC_004556.1.

Genome annotation databases

EnsemblBacteriaiAAO27988; AAO27988; PD_0088.
GeneIDi1144300.
KEGGixft:PD0088.
PATRICi24147572. VBIXylFas71109_0122.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009442 Genomic DNA. Translation: AAO27988.1.
RefSeqiNP_778339.1. NC_004556.1.

3D structure databases

ProteinModelPortaliQ87F49.
SMRiQ87F49. Positions 2-374.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi183190.PD0088.

Protein family/group databases

MEROPSiM20.010.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAO27988; AAO27988; PD_0088.
GeneIDi1144300.
KEGGixft:PD0088.
PATRICi24147572. VBIXylFas71109_0122.

Phylogenomic databases

eggNOGiCOG0624.
KOiK01439.
OMAiAGFACEH.
OrthoDBiEOG60651W.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00021.
BioCyciXFAS183190:GIX4-88-MONOMER.

Family and domain databases

Gene3Di3.30.70.360. 1 hit.
HAMAPiMF_01690. DapE.
InterProiIPR001261. ArgE/DapE_CS.
IPR005941. DapE_proteobac.
IPR002933. Peptidase_M20.
IPR011650. Peptidase_M20_dimer.
[Graphical view]
PfamiPF07687. M20_dimer. 1 hit.
PF01546. Peptidase_M20. 1 hit.
[Graphical view]
SUPFAMiSSF55031. SSF55031. 1 hit.
TIGRFAMsiTIGR01246. dapE_proteo. 1 hit.
PROSITEiPS00759. ARGE_DAPE_CPG2_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa."
    Van Sluys M.A., de Oliveira M.C., Monteiro-Vitorello C.B., Miyaki C.Y., Furlan L.R., Camargo L.E.A., da Silva A.C.R., Moon D.H., Takita M.A., Lemos E.G.M., Machado M.A., Ferro M.I.T., da Silva F.R., Goldman M.H.S., Goldman G.H., Lemos M.V.F., El-Dorry H., Tsai S.M.
    , Carrer H., Carraro D.M., de Oliveira R.C., Nunes L.R., Siqueira W.J., Coutinho L.L., Kimura E.T., Ferro E.S., Harakava R., Kuramae E.E., Marino C.L., Giglioti E., Abreu I.L., Alves L.M.C., do Amaral A.M., Baia G.S., Blanco S.R., Brito M.S., Cannavan F.S., Celestino A.V., da Cunha A.F., Fenille R.C., Ferro J.A., Formighieri E.F., Kishi L.T., Leoni S.G., Oliveira A.R., Rosa V.E. Jr., Sassaki F.T., Sena J.A.D., de Souza A.A., Truffi D., Tsukumo F., Yanai G.M., Zaros L.G., Civerolo E.L., Simpson A.J.G., Almeida N.F. Jr., Setubal J.C., Kitajima J.P.
    J. Bacteriol. 185:1018-1026(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Temecula1 / ATCC 700964.

Entry informationi

Entry nameiDAPE_XYLFT
AccessioniPrimary (citable) accession number: Q87F49
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 26, 2009
Last sequence update: June 1, 2003
Last modified: January 7, 2015
This is version 80 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. Peptidase families
    Classification of peptidase families and list of entries
  3. 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.