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Protein

Succinyl-diaminopimelate desuccinylase

Gene

dapE

Organism
Cronobacter sakazakii (strain ATCC BAA-894) (Enterobacter sakazakii)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

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.UniRule annotation

Catalytic activityi

N-succinyl-LL-2,6-diaminoheptanedioate + H2O = succinate + LL-2,6-diaminoheptanedioate.UniRule annotation

Cofactori

Protein has several cofactor binding sites:
  • Zn2+UniRule annotationNote: Binds 1 Zn2+ ion per subunit.UniRule annotation
  • Co2+UniRule annotationNote: Binds 1 Co2+ ion per subunit.UniRule annotation

Pathwayi: L-lysine biosynthesis via DAP pathway

This protein is involved in step 3 of the subpathway that synthesizes LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (succinylase route).UniRule annotation
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (dapD)
  2. Acetylornithine/succinyldiaminopimelate aminotransferase (argD), Acetylornithine/succinyldiaminopimelate aminotransferase (argD)
  3. Succinyl-diaminopimelate desuccinylase (dapE)
This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (succinylase route), the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi66Cobalt or zinc 1UniRule annotation1
Active sitei68UniRule annotation1
Metal bindingi99Cobalt or zinc 1UniRule annotation1
Metal bindingi99Cobalt or zinc 2UniRule annotation1
Active sitei133Proton acceptorUniRule annotation1
Metal bindingi134Cobalt or zinc 2UniRule annotation1
Metal bindingi162Cobalt or zinc 1UniRule annotation1
Metal bindingi348Cobalt or zinc 2UniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Amino-acid biosynthesis, Diaminopimelate biosynthesis, Lysine biosynthesis

Keywords - Ligandi

Cobalt, Metal-binding, Zinc

Enzyme and pathway databases

UniPathwayiUPA00034; UER00021.

Protein family/group databases

MEROPSiM20.010.

Names & Taxonomyi

Protein namesi
Recommended name:
Succinyl-diaminopimelate desuccinylaseUniRule annotation (EC:3.5.1.18UniRule annotation)
Short name:
SDAP desuccinylaseUniRule annotation
Alternative name(s):
N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolaseUniRule annotation
Gene namesi
Name:dapEUniRule annotation
Ordered Locus Names:ESA_00778
OrganismiCronobacter sakazakii (strain ATCC BAA-894) (Enterobacter sakazakii)
Taxonomic identifieri290339 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeCronobacter
Proteomesi
  • UP000000260 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003755481 – 375Succinyl-diaminopimelate desuccinylaseAdd BLAST375

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi290339.ESA_00778.

Structurei

3D structure databases

ProteinModelPortaliA7ML10.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase M20A family. DapE subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C9Y. Bacteria.
COG0624. LUCA.
HOGENOMiHOG000243770.
KOiK01439.
OMAiRHQLNYT.

Family and domain databases

CDDicd03891. M20_DapE_proteobac. 1 hit.
Gene3Di3.30.70.360. 1 hit.
HAMAPiMF_01690. DapE. 1 hit.
InterProiIPR001261. ArgE/DapE_CS.
IPR005941. DapE_proteobac.
IPR002933. Peptidase_M20.
IPR011650. Peptidase_M20_dimer.
[Graphical view]
PfamiPF07687. M20_dimer. 1 hit.
PF01546. Peptidase_M20. 1 hit.
[Graphical view]
SUPFAMiSSF55031. SSF55031. 1 hit.
TIGRFAMsiTIGR01246. dapE_proteo. 1 hit.
PROSITEiPS00758. ARGE_DAPE_CPG2_1. 1 hit.
PS00759. ARGE_DAPE_CPG2_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A7ML10-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSCPVIELTQ QLIRRPSLSP DDAGCQALLI ERLQAVGFTV EPMNIGDTQN
60 70 80 90 100
FWAWRGTGET LAFAGHTDVV PAGDVERWIN PPFEPTIRDG MLFGRGAADM
110 120 130 140 150
KGSLAAMVVA AERFVAQHPH HRGRLAFLIT SDEEASATNG TVKVVEALMA
160 170 180 190 200
RGERLDYCLV GEPSSSEVVG DVVKNGRRGS LTCNLTIHGV QGHVAYPHLA
210 220 230 240 250
DNPVHRAAPM LNELVGIEWD RGNEFFPPTS MQIANIQAGT GSNNVIPGDL
260 270 280 290 300
HVQFNFRFST ELTDEMIKQR VVALLEKYQL RYTLDWWLSG QPFLTARGKL
310 320 330 340 350
VDAVVNAVHH YNEIKPQLLT TGGTSDGRFI ARMGAQVVEL GPVNATIHKI
360 370
NECVKASDLQ LLARMYQRIM EQLVA
Length:375
Mass (Da):41,244
Last modified:October 2, 2007 - v1
Checksum:i5F4EB07003167BEF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000783 Genomic DNA. Translation: ABU76055.1.
RefSeqiWP_012124066.1. NC_009778.1.

Genome annotation databases

EnsemblBacteriaiABU76055; ABU76055; ESA_00778.
GeneIDi5550571.
KEGGiesa:ESA_00778.
PATRICi20393765. VBICroSak107175_0690.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000783 Genomic DNA. Translation: ABU76055.1.
RefSeqiWP_012124066.1. NC_009778.1.

3D structure databases

ProteinModelPortaliA7ML10.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi290339.ESA_00778.

Protein family/group databases

MEROPSiM20.010.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABU76055; ABU76055; ESA_00778.
GeneIDi5550571.
KEGGiesa:ESA_00778.
PATRICi20393765. VBICroSak107175_0690.

Phylogenomic databases

eggNOGiENOG4105C9Y. Bacteria.
COG0624. LUCA.
HOGENOMiHOG000243770.
KOiK01439.
OMAiRHQLNYT.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00021.

Family and domain databases

CDDicd03891. M20_DapE_proteobac. 1 hit.
Gene3Di3.30.70.360. 1 hit.
HAMAPiMF_01690. DapE. 1 hit.
InterProiIPR001261. ArgE/DapE_CS.
IPR005941. DapE_proteobac.
IPR002933. Peptidase_M20.
IPR011650. Peptidase_M20_dimer.
[Graphical view]
PfamiPF07687. M20_dimer. 1 hit.
PF01546. Peptidase_M20. 1 hit.
[Graphical view]
SUPFAMiSSF55031. SSF55031. 1 hit.
TIGRFAMsiTIGR01246. dapE_proteo. 1 hit.
PROSITEiPS00758. ARGE_DAPE_CPG2_1. 1 hit.
PS00759. ARGE_DAPE_CPG2_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDAPE_CROS8
AccessioniPrimary (citable) accession number: A7ML10
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 26, 2009
Last sequence update: October 2, 2007
Last modified: November 2, 2016
This is version 60 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.