Succinyl-diaminopimelate desuccinylase - Agrobacterium tumefaciens (strain C58 / ATCC 33970)

Contribute

Send feedback

Read comments (?) or add your own

A9CKC4 (DAPE_AGRT5) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 39. History...

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

Documents (3) |

Third-party data

text xml rdf/xml gff fasta

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:	Atu0370
ORF Names:	AGR_C_647

Organism

Agrobacterium tumefaciens (strain C58 / ATCC 33970) [Reference proteome] [HAMAP]

Taxonomic identifier

176299 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Rhizobiaceae › Rhizobium/Agrobacterium group › Agrobacterium › Agrobacterium tumefaciens complex ›

Protein attributes

Sequence length	398 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 Reference 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 – 398

398

Succinyl-diaminopimelate desuccinylase HAMAP-Rule MF_01690

PRO_0000375456

Sites

Active site

By similarity

Active site

140

Proton acceptor By similarity

Metal binding

Cobalt or zinc 1 By similarity

Metal binding

106

Cobalt or zinc 1 By similarity

Metal binding

106

Cobalt or zinc 2 By similarity

Metal binding

141

Cobalt or zinc 2 By similarity

Metal binding

169

Cobalt or zinc 1 By similarity

Metal binding

366

Cobalt or zinc 2 By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

A9CKC4 [UniParc].

Last modified January 15, 2008. Version 1.
Checksum: 5A2BDEEB188CEFB9
Show »

FASTA

398

42,547

        10         20         30         40         50         60 
MTTTDPVANL AALIRCPSVT PAEGGALSLL DTLLSPLGFA VERVMATEDG TPDVENLYAR 

        70         80         90        100        110        120 
LGTEGPHLMF AGHTDVVPVG DEAAWSHPPF SADIAGGEMY GRGAVDMKGG IACFVAAIAR 

       130        140        150        160        170        180 
HIGKHGKPQG SVSFLITGDE EGPSINGTSK LLEWAAAKGE TWDACVVGEP TNPDQLGDMI 

       190        200        210        220        230        240 
KIGRRGSLSG RITVQGVQGH AAYPHLADNP IRGLLQLTHA LMHPAFDHGT DDFQPSNLEV 

       250        260        270        280        290        300 
TTVDTGNAAT NVIPARATAA FNIRFNDSWT AESLRAEIIR RLDAAANEGE LRPDRAPVKY 

       310        320        330        340        350        360 
EIVWADRPSH VFLTRNNALI SSLSGAIETV TGKEPKLSTT GGTSDARFIK DYCPVVEFGL 

       370        380        390 
VGQTMHMVDE RVAVADLETL TRIYETFIER WFAHADGK

« Hide

References

[1]

"Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58."
Goodner B., Hinkle G., Gattung S., Miller N., Blanchard M., Qurollo B., Goldman B.S., Cao Y., Askenazi M., Halling C., Mullin L., Houmiel K., Gordon J., Vaudin M., Iartchouk O., Epp A., Liu F., Wollam C.

Slater S.
Science 294:2323-2328(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: C58 / ATCC 33970.

[2]

"The genome of the natural genetic engineer Agrobacterium tumefaciens C58."
Wood D.W., Setubal J.C., Kaul R., Monks D.E., Kitajima J.P., Okura V.K., Zhou Y., Chen L., Wood G.E., Almeida N.F. Jr., Woo L., Chen Y., Paulsen I.T., Eisen J.A., Karp P.D., Bovee D. Sr., Chapman P., Clendenning J.

Nester E.W.
Science 294:2317-2323(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: C58 / ATCC 33970.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE007869 Genomic DNA. Translation: AAK86187.1.
PIR	AB2622. B97404.
RefSeq	NP_353402.1. NC_003062.2.
3D structure databases
ProteinModelPortal	A9CKC4.
ModBase	Search...
Protein-protein interaction databases
STRING	176299.Atu0370.
Protein family/group databases
MEROPS	M20.010.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	1132408.
KEGG	atu:Atu0370.
PATRIC	20810423. VBIAgrTum91616_0361.
Phylogenomic databases
eggNOG	COG0624.
HOGENOM	HOG000243770.
KO	K01439.
OMA	WDAPRLE.
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. 1 hit. PS00759. ARGE_DAPE_CPG2_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DAPE_AGRT5

Accession

Primary (citable) accession number: A9CKC4

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 26, 2009
Last sequence update:	January 15, 2008
Last modified:	May 1, 2013
This is version 39 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

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents