B1Y6E7 (DAPE_LEPCP) Reviewed, UniProtKB/Swiss-Prot

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:	Lcho_2518

Organism

Leptothrix cholodnii (strain ATCC 51168 / LMG 8142 / SP-6) (Leptothrix discophora (strain SP-6)) [Complete proteome] [HAMAP]

Taxonomic identifier

395495 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Betaproteobacteria › Burkholderiales › unclassified Burkholderiales › Burkholderiales Genera incertae sedis › Leptothrix › Leptothrix cholodnii

Protein attributes

Sequence length	382 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
Molecular_function	cobalt ion binding Inferred from electronic annotation. Source: HAMAP 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 – 382	382	Succinyl-diaminopimelate desuccinylase HAMAP-Rule MF_01690		PRO_0000375602
Sites
	Active site	75	1	By similarity
	Active site	140	1	Proton acceptor By similarity
	Metal binding	73	1	Cobalt or zinc 1 By similarity
	Metal binding	106	1	Cobalt or zinc 1 By similarity
	Metal binding	106	1	Cobalt or zinc 2 By similarity
	Metal binding	141	1	Cobalt or zinc 2 By similarity
	Metal binding	169	1	Cobalt or zinc 1 By similarity
	Metal binding	355	1	Cobalt or zinc 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	B1Y6E7 [UniParc]. Last modified May 20, 2008. Version 1. Checksum: 40A18D0CC9D4F954	FASTA	382	41,013
	10 20 30 40 50 60 MHLPTLSLVE ELIARRSVTP DDAGCQALIA ARLAALGFEI HALPHGPADA RVDNLWAIRR 70 80 90 100 110 120 GQGDGPTLVL AGHTDVVPTG PLERWHSDPF VPSHRAGLLY GRGAADMKTS LAAMVVAVEE 130 140 150 160 170 180 FVAAHPVHRG SVAFLLTSDE EGPAVDGTVK VCEWLAARGE RLDACIVGEP TSVRQLGDMI 190 200 210 220 230 240 KNGRRGSLSG RLTVVGQQGH IAYPHLARNP IHLAAPALAE LAQQRWDDGN EHFPPTSWQM 250 260 270 280 290 300 SNIHAGTGAT NVIPGELVVD FNFRFSTEST PESLQQQVHA LLDRHGLEHR IAWTLGGRPF 310 320 330 340 350 360 LTRPGSLTDA LSQAITAVTG LRTELSTTGG TSDGRFIAQI CPQVVEFGPV NATIHQVDEH 370 380 CEVAALGPLK DIYRRTLEAM LA

References

[1]

"Complete sequence of Leptothrix cholodnii SP-6." US DOE Joint Genome Institute Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Chertkov O., Brettin T., Detter J.C., Han C., Kuske C.R., Schmutz J., Larimer F., Land M., Hauser L. , Kyrpides N., Lykidis A., Emerson D., Richardson P. Submitted (MAR-2008) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 51168 / LMG 8142 / SP-6.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP001013 Genomic DNA. Translation: ACB34783.1.
RefSeq	YP_001791548.1. NC_010524.1.
3D structure databases
ProteinModelPortal	B1Y6E7.
SMR	B1Y6E7. Positions 4-381.
ModBase	Search...
Protein-protein interaction databases
STRING	395495.Lcho_2518.
Protein family/group databases
MEROPS	M20.010.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	ACB34783; ACB34783; Lcho_2518.
GeneID	6161483.
KEGG	lch:Lcho_2518.
PATRIC	22395409. VBILepCho83238_2538.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0624.
HOGENOM	HOG000243770.
KO	K01439.
OMA	WDAPRLE.
ProtClustDB	PRK13009.
Enzyme and pathway databases
BioCyc	LCHO395495:GHYL-2555-MONOMER.
UniPathway	UPA00034; UER00021.
Family and domain databases
HAMAP	MF_01690. DapE.
InterPro	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. False negative. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DAPE_LEPCP

Accession

Primary (citable) accession number: B1Y6E7

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 26, 2009
Last sequence update:	May 20, 2008
Last modified:	May 1, 2013
This is version 36 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program