Succinyl-diaminopimelate desuccinylase - Xylella fastidiosa (strain Temecula1 / ATCC 700964)

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Q87F49 (DAPE_XYLFT) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 72. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Succinyl-diaminopimelate desuccinylase
Short name=SDAP desuccinylase
EC=3.5.1.18

Alternative name(s):
N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase

Gene names

Name:	dapE
Ordered Locus Names:	PD_0088

Organism

Xylella fastidiosa (strain Temecula1 / ATCC 700964) [Complete proteome] [HAMAP]

Taxonomic identifier

183190 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Xanthomonadales › Xanthomonadaceae › Xylella ›

Protein attributes

Sequence length	377 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	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 By similarity. HAMAP-Rule MF_01690
Catalytic activity	N-succinyl-LL-2,6-diaminoheptanedioate + H₂O = succinate + LL-2,6-diaminoheptanedioate. HAMAP-Rule MF_01690
Cofactor	Binds 1 Zn²⁺ ion per subunit By similarity. Binds 1 Co²⁺ ion per subunit By similarity.
Pathway	Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (succinylase route): step 3/3. HAMAP-Rule MF_01690
Subunit structure	Homodimer By similarity.
Sequence similarities	Belongs to the peptidase M20A family. DapE subfamily.

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Diaminopimelate biosynthesis Lysine biosynthesis
Ligand	Cobalt Metal-binding Zinc
Molecular function	Hydrolase
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	diaminopimelate biosynthetic process Inferred from electronic annotation. Source: HAMAP lysine biosynthetic process via diaminopimelate Inferred from electronic annotation. Source: HAMAP proteolysis Inferred from electronic annotation. Source: InterPro
Molecular_function	cobalt ion binding Inferred from electronic annotation. Source: HAMAP metallopeptidase activity Inferred from electronic annotation. Source: InterPro succinyl-diaminopimelate desuccinylase activity Inferred from electronic annotation. Source: HAMAP zinc ion binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 377

377

Succinyl-diaminopimelate desuccinylase HAMAP-Rule MF_01690

PRO_0000375792

Sites

Active site

By similarity

Active site

133

Proton acceptor By similarity

Metal binding

Cobalt or zinc 1 By similarity

Metal binding

Cobalt or zinc 1 By similarity

Metal binding

Cobalt or zinc 2 By similarity

Metal binding

134

Cobalt or zinc 2 By similarity

Metal binding

162

Cobalt or zinc 1 By similarity

Metal binding

348

Cobalt or zinc 2 By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

Q87F49 [UniParc].

Last modified June 1, 2003. Version 1.
Checksum: 7269AD1D6B67C98F
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FASTA

377

40,992

        10         20         30         40         50         60 
MSDVLDLACD LISRPSMTPD DAGCQEMIAK RLERAGFICE HLRYAAVSNL WATHGRGAPV 

        70         80         90        100        110        120 
LVLLGHTDVV PPGPVEAWTS DPFMPDMRNG ILYGRGAADM KGSVAAFVIA AERFLAAYPQ 

       130        140        150        160        170        180 
HPGTLAILLT SDEEGQAIDG VRKVAETLRQ RGQGIDWCLT GEPSSSKRLG DLLRVGRRGS 

       190        200        210        220        230        240 
LSATLHVKGV QGHVAYPHQA RNPIHLALPA FAALTARHWD DGYESFPSTS LQISNIHAGT 

       250        260        270        280        290        300 
GANNVIPGAL EVAFNLRYNP HWIAPRLESE IVALLDQHGL DYTLHWHRSG EPFYTPEGKL 

       310        320        330        340        350        360 
RRIAREVLER FSGAPPEEST GGGTSDARFI APLGAQCIEV GPVNASIHQV DEHVCLSDLE 

       370 
ALPDLYQLLI ERLLAEH

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References

[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.

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.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE009442 Genomic DNA. Translation: AAO27988.1.
RefSeq	NP_778339.1. NC_004556.1.
3D structure databases
ProteinModelPortal	Q87F49.
SMR	Q87F49. Positions 2-374.
ModBase	Search...
Protein-protein interaction databases
STRING	183190.PD0088.
Protein family/group databases
MEROPS	M20.010.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAO27988; AAO27988; PD_0088.
GeneID	1144300.
KEGG	xft:PD0088.
PATRIC	24147572. VBIXylFas71109_0122.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0624.
KO	K01439.
OMA	MWARRGN.
ProtClustDB	PRK13009.
Enzyme and pathway databases
UniPathway	UPA00034; UER00021.
Family and domain databases
HAMAP	MF_01690. DapE.
InterPro	IPR001261. ArgE/DapE_CS. IPR005941. DapE_proteobac. IPR002933. Peptidase_M20. IPR011650. Peptidase_M20_dimer. [Graphical view]
Pfam	PF07687. M20_dimer. 1 hit. PF01546. Peptidase_M20. 1 hit. [Graphical view]
SUPFAM	SSF55031. Peptidase_M20_dimer. 1 hit.
TIGRFAMs	TIGR01246. dapE_proteo. 1 hit.
PROSITE	PS00758. ARGE_DAPE_CPG2_1. False negative. PS00759. ARGE_DAPE_CPG2_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DAPE_XYLFT

Accession

Primary (citable) accession number: Q87F49

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 26, 2009
Last sequence update:	June 1, 2003
Last modified:	May 1, 2013
This is version 72 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Peptidase families

Classification of peptidase families and list of entries

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protein family/group databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents