Succinyl-diaminopimelate desuccinylase - Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

Contribute

Send feedback

Read comments (?) or add your own

Q8ZN75 (DAPE_SALTY) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 69. 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):
Aspartyl peptidase
N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase

Gene names

Name:	dapE
Ordered Locus Names:	STM2483

Organism

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) [Reference proteome] [HAMAP]

Taxonomic identifier

99287 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Salmonella ›

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. Can also hydrolyze all N-terminal Asp dipeptides except Asp-Pro. Asp-Ser is the best substrate, followed by Asp-Gly, Asp-Leu, and Asp-Cys. Ref.2
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.2 Binds 1 Co²⁺ ion per subunit for desuccinylase activity. Ref.2 Binds 1 Mn²⁺ ion per subunit for peptidase activity. Ref.2
Enzyme regulation	Mn²⁺-activated peptidase is inhibited by Mn²⁺ at concentration above 1 mM and by increasing concnentrations of Co²⁺. There is a competitive inhibitor effect between the substrates. Hydrolysis of Asp-Leu by Mn²⁺-activated DapE is inhibited by SDAP, and hydrolysis of SDAP by Co²⁺-activated DapE is inhibited by Asp-Ser. Ref.2
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.
Miscellaneous	Zn(+2) is usually found in the tight binding site, but the nature of the second cation in the low affinity binding site is different according the activity. HAMAP-Rule MF_01690
Sequence similarities	Belongs to the peptidase M20A family. DapE subfamily.
Biophysicochemical properties	Kinetic parameters: K_M=0.63 mM for SDAP (in the presence of 1 mM Co²⁺ Ref.2 K_M=0.66 mM for Asp-Ser (in the presence of 1 mM Mn²⁺ K_M=3.3 mM for Asp-Leu (in the presence of 1 mM Mn²⁺

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Diaminopimelate biosynthesis Lysine biosynthesis
Ligand	Cobalt Manganese Metal-binding Zinc
Molecular function	Dipeptidase Hydrolase Metalloprotease Protease
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: UniProtKB-KW
Molecular_function	cobalt ion binding Inferred from electronic annotation. Source: HAMAP dipeptidase activity Inferred from electronic annotation. Source: UniProtKB-KW metallopeptidase activity Inferred from electronic annotation. Source: UniProtKB-KW 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 – 375

375

Succinyl-diaminopimelate desuccinylase HAMAP-Rule MF_01690

PRO_0000375723

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

Q8ZN75 [UniParc].

Last modified March 1, 2002. Version 1.
Checksum: ED6165EDEEB262A0
Show »

FASTA

375

41,578

        10         20         30         40         50         60 
MSCPVIELTQ QLIRRPSLSP DDAGCQALMI ERLRKIGFTI EHMDFGDTQN FWAWRGRGET 

        70         80         90        100        110        120 
LAFAGHTDVV PAGDVDRWIN PPFEPTIRDG MLFGRGAADM KGSLAAMVVA AERFVAQHPH 

       130        140        150        160        170        180 
HRGRLAFLIT SDEEASAKNG TVKVVEALMA RNERLDYCLV GEPSSTEIVG DVVKNGRRGS 

       190        200        210        220        230        240 
LTCNLTIHGV QGHVAYPHLA DNPVHRAAPF LNELVAIEWD RGNDFFPATS MQVANIQAGT 

       250        260        270        280        290        300 
GSNNVIPGEL FVQFNFRFST ELTDEMIKER VHALLEKHQL RYTVDWWLSG QPFLTARGKL 

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

       370 
LLARMYQRIM EQLVA

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete genome sequence of Salmonella enterica serovar Typhimurium LT2." McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P., Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D., Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E. Wilson R.K. Nature 413:852-856(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: LT2 / SGSC1412 / ATCC 700720.
[2]	"DapE can function as an aspartyl peptidase in the presence of Mn2+." Broder D.H., Miller C.G. J. Bacteriol. 185:4748-4754(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, COFACTOR, SUBSTRATE SPECIFICITY.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE006468 Genomic DNA. Translation: AAL21377.1.
RefSeq	NP_461418.1. NC_003197.1.
3D structure databases
ProteinModelPortal	Q8ZN75.
SMR	Q8ZN75. Positions 4-374.
ModBase	Search...
Protein-protein interaction databases
STRING	99287.STM2483.
Proteomic databases
PaxDb	Q8ZN75.
PRIDE	Q8ZN75.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAL21377; AAL21377; STM2483.
GeneID	1254005.
KEGG	stm:STM2483.
PATRIC	32383597. VBISalEnt20916_2621.
Phylogenomic databases
eggNOG	COG0624.
HOGENOM	HOG000243770.
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. 1 hit. PS00759. ARGE_DAPE_CPG2_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DAPE_SALTY

Accession

Primary (citable) accession number: Q8ZN75

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 26, 2009
Last sequence update:	March 1, 2002
Last modified:	May 1, 2013
This is version 69 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

Proteomic databases

Protocols and materials databases

Genome annotation databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents