Succinyl-diaminopimelate desuccinylase - Escherichia coli (strain K12)

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P0AED7 (DAPE_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 65. History...

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

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·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
Synonyms:	msgB
Ordered Locus Names:	b2472, JW2456

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	375 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

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. Ref.6
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. Ref.6 Binds 1 Co²⁺ ion per subunit. Ref.6
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. Ref.6
Miscellaneous	DapE/msgB is a multicopy suppressor of a temperature-sensitive allele of the heat shock gene grpE. HAMAP-Rule MF_01690
Sequence similarities	Belongs to the peptidase M20A family. DapE subfamily.
Biophysicochemical properties	Kinetic parameters: K_M=0.41 mM for L,L-SDAP (in the presence of Zn²⁺ at pH 7.0) Ref.6

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 mutant phenotype Ref.1. Source: EcoliWiki zinc ion binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
groL	P0A6F5	1	EBI-1129009,EBI-543750
hemX	P09127	1	EBI-1129009,EBI-1128342

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 375

375

Succinyl-diaminopimelate desuccinylase HAMAP-Rule MF_01690

PRO_0000185261

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

P0AED7 [UniParc].

Last modified December 6, 2005. Version 1.
Checksum: 181F43D05E88C20E
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FASTA

375

41,269

        10         20         30         40         50         60 
MSCPVIELTQ QLIRRPSLSP DDAGCQALLI ERLQAIGFTV ERMDFADTQN FWAWRGQGET 

        70         80         90        100        110        120 
LAFAGHTDVV PPGDADRWIN PPFEPTIRDG MLFGRGAADM KGSLAAMVVA AERFVAQHPN 

       130        140        150        160        170        180 
HTGRLAFLIT SDEEASAHNG TVKVVEALMA RNERLDYCLV GEPSSIEVVG DVVKNGRRGS 

       190        200        210        220        230        240 
LTCNLTIHGV QGHVAYPHLA DNPVHRAAPF LNELVAIEWD QGNEFFPATS MQIANIQAGT 

       250        260        270        280        290        300 
GSNNVIPGEL FVQFNFRFST ELTDEMIKAQ VLALLEKHQL RYTVDWWLSG QPFLTARGKL 

       310        320        330        340        350        360 
VDAVVNAVEH YNEIKPQLLT TGGTSDGRFI ARMGAQVVEL GPVNATIHKI NECVNAADLQ 

       370 
LLARMYQRIM EQLVA

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning, characterization, and expression of the dapE gene of Escherichia coli." Bouvier J., Richaud C., Higgins W., Bogler O., Stragier S. J. Bacteriol. 174:5265-5271(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"The essential Escherichia coli msgB gene, a multicopy suppressor of a temperature-sensitive allele of the heat shock gene grpE, is identical to dapE." Wu B., Georgopoulos C., Ang D. J. Bacteriol. 174:5258-5264(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features." Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T. Horiuchi T. DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"Bacterial N-succinyl-L-diaminopimelic acid desuccinylase. Purification, partial characterization, and substrate specificity." Lin Y.K., Myhrman R., Schrag M.L., Gelb M.H. J. Biol. Chem. 263:1622-1627(1988) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBUNIT, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.

Cross-references

Sequence databases
EMBL GenBank DDBJ	S41760 Genomic DNA. Translation: AAB22798.1. X57403 Genomic DNA. Translation: CAA40665.1. U00096 Genomic DNA. Translation: AAC75525.1. AP009048 Genomic DNA. Translation: BAA16346.1.
PIR	A42959.
RefSeq	NP_416967.1. NC_000913.2. YP_490699.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P0AED7.
SMR	P0AED7. Positions 1-375.
ModBase	Search...
Protein-protein interaction databases
IntAct	P0AED7. 3 interactions.
STRING	511145.b2472.
Protein family/group databases
MEROPS	M20.010.
Proteomic databases
PaxDb	P0AED7.
PRIDE	P0AED7.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC75525; AAC75525; b2472. BAA16346; BAA16346; BAA16346.
GeneID	12932722. 948313.
KEGG	ecj:Y75_p2424. eco:b2472.
PATRIC	32120327. VBIEscCol129921_2566.
Organism-specific databases
EchoBASE	EB0204.
EcoGene	EG10208. dapE.
Phylogenomic databases
eggNOG	COG0624.
HOGENOM	HOG000243770.
KO	K01439.
OMA	MWARRGN.
ProtClustDB	PRK13009.
Enzyme and pathway databases
BioCyc	EcoCyc:MONOMER0-1981. ECOL316407:JW2456-MONOMER. MetaCyc:MONOMER0-1981.
SABIO-RK	P0AED7.
UniPathway	UPA00034; UER00021.
Gene expression databases
Genevestigator	P0AED7.
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_ECOLI

Accession

Primary (citable) accession number: P0AED7
Secondary accession number(s): P24176

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 6, 2005
Last sequence update:	December 6, 2005
Last modified:	May 1, 2013
This is version 65 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

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

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

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protein family/group databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents