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Protein

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Gene

dapD

Organism
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of the cyclic tetrahydrodipicolinate (THDP) into the acyclic N-succinyl-L-2-amino-6-oxopimelate using succinyl-CoA (By similarity). Displays succinyl transferase activity with L-2-aminopimelate and succinyl-CoA as substrates (PubMed:22359568).UniRule annotation1 Publication

Catalytic activityi

Succinyl-CoA + (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + H2O = CoA + N-succinyl-L-2-amino-6-oxoheptanedioate.UniRule annotation

Cofactori

Note: Magnesium ions are not essential for catalysis.1 Publication

Enzyme regulationi

Weakly inhibited by D-2-aminopimelate.1 Publication

Kineticsi

  1. KM=7 mM for L-2-aminopimelate1 Publication
  1. Vmax=105 µmol/min/mg enzyme1 Publication

Pathwayi: L-lysine biosynthesis via DAP pathway

This protein is involved in step 1 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. no protein annotated in this organism
  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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi205 – 2051Magnesium; shared with trimeric partnersUniRule annotation
Active sitei221 – 2211Acyl-anhydride intermediateUniRule annotation
Binding sitei223 – 2231Succinyl-CoA1 Publication
Binding sitei238 – 2381Succinyl-CoA; via amide nitrogen1 Publication
Binding sitei241 – 2411Succinyl-CoA1 Publication
Binding sitei264 – 2641Succinyl-CoA; via amide nitrogen1 Publication
Binding sitei304 – 3041Succinyl-CoA1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Acyltransferase, Transferase

Keywords - Biological processi

Amino-acid biosynthesis, Diaminopimelate biosynthesis, Lysine biosynthesis

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

UniPathwayiUPA00034; UER00019.

Names & Taxonomyi

Protein namesi
Recommended name:
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferaseUniRule annotation (EC:2.3.1.117UniRule annotation)
Alternative name(s):
Tetrahydrodipicolinate N-succinyltransferaseUniRule annotation
Short name:
THDP succinyltransferaseUniRule annotation
Short name:
THP succinyltransferaseUniRule annotation
Tetrahydropicolinate succinylaseUniRule annotation
Gene namesi
Name:dapDUniRule annotation
Ordered Locus Names:PA3666
OrganismiPseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Taxonomic identifieri208964 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
Proteomesi
  • UP000002438 Componenti: Chromosome

Organism-specific databases

PseudoCAPiPA3666.

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 3443442,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferasePRO_0000421301Add
BLAST

Proteomic databases

PaxDbiG3XD76.

2D gel databases

World-2DPAGE0008:Q9Z9H2.

Interactioni

Subunit structurei

Homotrimer.1 Publication

Protein-protein interaction databases

STRINGi208964.PA3666.

Structurei

Secondary structure

1
344
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 1510Combined sources
Beta strandi21 – 288Combined sources
Beta strandi30 – 323Combined sources
Helixi35 – 4511Combined sources
Beta strandi49 – 568Combined sources
Helixi58 – 6811Combined sources
Turni69 – 713Combined sources
Helixi73 – 8311Combined sources
Beta strandi89 – 968Combined sources
Helixi103 – 11412Combined sources
Helixi128 – 1314Combined sources
Beta strandi135 – 1384Combined sources
Beta strandi141 – 1444Combined sources
Helixi145 – 15713Combined sources
Beta strandi164 – 1707Combined sources
Helixi173 – 1753Combined sources
Beta strandi182 – 1865Combined sources
Helixi187 – 1893Combined sources
Beta strandi194 – 1963Combined sources
Beta strandi200 – 2023Combined sources
Beta strandi212 – 2209Combined sources
Beta strandi222 – 2243Combined sources
Beta strandi234 – 2363Combined sources
Beta strandi267 – 2704Combined sources
Beta strandi289 – 2935Combined sources
Beta strandi299 – 3046Combined sources
Helixi305 – 3084Combined sources
Beta strandi315 – 3184Combined sources
Turni320 – 3223Combined sources
Beta strandi325 – 3284Combined sources
Helixi333 – 3419Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3R5AX-ray1.89A/B/C/D/E/F1-344[»]
3R5BX-ray2.51A/B/C/D/E/F1-344[»]
3R5CX-ray2.40A/B/C1-344[»]
3R5DX-ray1.80A/B/C/D/E/F1-344[»]
ProteinModelPortaliG3XD76.
SMRiG3XD76. Positions 1-342.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni279 – 2802Succinyl-CoA binding1 Publication
Regioni287 – 2893Succinyl-CoA binding1 Publication
Regioni317 – 3204Succinyl-CoA binding1 Publication

Sequence similaritiesi

Belongs to the type 2 tetrahydrodipicolinate N-succinyltransferase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105EJ3. Bacteria.
COG2171. LUCA.
InParanoidiG3XD76.
KOiK00674.
OMAiKHANNLY.
OrthoDBiEOG6HQSR3.
PhylomeDBiG3XD76.

Family and domain databases

Gene3Di3.30.60.70. 1 hit.
HAMAPiMF_02122. DapD_type2.
InterProiIPR019876. DapD_gammaproteobac.
IPR001451. Hexapep.
IPR032784. THDPS_M.
IPR011004. Trimer_LpxA-like.
IPR026586. Type2_DapD.
[Graphical view]
PfamiPF14602. Hexapep_2. 1 hit.
PF14789. THDPS_M. 1 hit.
[Graphical view]
SUPFAMiSSF51161. SSF51161. 1 hit.
TIGRFAMsiTIGR03536. DapD_gpp. 1 hit.

Sequencei

Sequence statusi: Complete.

G3XD76-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSQSLFSLAF GVGTQNRQEA WLEVFYALPL LKPSSEIVAA VAPILGYAAG
60 70 80 90 100
NQALTFTSQQ AYQLADALKG IDAAQSALLS RLAESQKPLV ATLLAEDAAP
110 120 130 140 150
SSTAEAYLKL HLLSHRLVKP HAVNLSGIFP LLPNVAWTNI GAVDLAELAE
160 170 180 190 200
LQLEARLKGK LLEVFSVDKF PKMTDYVVPA GVRIADTARV RLGAYIGEGT
210 220 230 240 250
TVMHEGFVNF NAGTEGPGMI EGRVSAGVFV GKGSDLGGGC STMGTLSGGG
260 270 280 290 300
NIVISVGEGC LIGANAGIGI PLGDRNIVEA GLYITAGTKV ALLDEQNALV
310 320 330 340
KVVKARDLAG QPDLLFRRNS QNGAVECKTN KTAIELNEAL HAHN
Length:344
Mass (Da):35,973
Last modified:November 16, 2011 - v1
Checksum:iCF80600C50A316F2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB024601 Genomic DNA. Translation: BAA75911.1.
AE004091 Genomic DNA. Translation: AAG07054.1.
PIRiE83187.
RefSeqiNP_252356.1. NC_002516.2.
WP_003113860.1. NZ_ASJY01000592.1.

Genome annotation databases

EnsemblBacteriaiAAG07054; AAG07054; PA3666.
GeneIDi880584.
KEGGipae:PA3666.
PATRICi19841955. VBIPseAer58763_3835.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB024601 Genomic DNA. Translation: BAA75911.1.
AE004091 Genomic DNA. Translation: AAG07054.1.
PIRiE83187.
RefSeqiNP_252356.1. NC_002516.2.
WP_003113860.1. NZ_ASJY01000592.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3R5AX-ray1.89A/B/C/D/E/F1-344[»]
3R5BX-ray2.51A/B/C/D/E/F1-344[»]
3R5CX-ray2.40A/B/C1-344[»]
3R5DX-ray1.80A/B/C/D/E/F1-344[»]
ProteinModelPortaliG3XD76.
SMRiG3XD76. Positions 1-342.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi208964.PA3666.

2D gel databases

World-2DPAGE0008:Q9Z9H2.

Proteomic databases

PaxDbiG3XD76.

Protocols and materials databases

DNASUi880584.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAG07054; AAG07054; PA3666.
GeneIDi880584.
KEGGipae:PA3666.
PATRICi19841955. VBIPseAer58763_3835.

Organism-specific databases

PseudoCAPiPA3666.

Phylogenomic databases

eggNOGiENOG4105EJ3. Bacteria.
COG2171. LUCA.
InParanoidiG3XD76.
KOiK00674.
OMAiKHANNLY.
OrthoDBiEOG6HQSR3.
PhylomeDBiG3XD76.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00019.

Family and domain databases

Gene3Di3.30.60.70. 1 hit.
HAMAPiMF_02122. DapD_type2.
InterProiIPR019876. DapD_gammaproteobac.
IPR001451. Hexapep.
IPR032784. THDPS_M.
IPR011004. Trimer_LpxA-like.
IPR026586. Type2_DapD.
[Graphical view]
PfamiPF14602. Hexapep_2. 1 hit.
PF14789. THDPS_M. 1 hit.
[Graphical view]
SUPFAMiSSF51161. SSF51161. 1 hit.
TIGRFAMsiTIGR03536. DapD_gpp. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "P.aeruginosa PAO1."
    Nashimoto H.
    Submitted (MAR-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228.
  3. "Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion."
    Schnell R., Oehlmann W., Sandalova T., Braun Y., Huck C., Maringer M., Singh M., Schneider G.
    PLoS ONE 7:E31133-E31133(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF APOENZYME AND IN COMPLEXES WITH SUCCINATE; COA AND 2-AMINOPIMELATE, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, ENZYME REGULATION, SUBUNIT.

Entry informationi

Entry nameiDAPD_PSEAE
AccessioniPrimary (citable) accession number: G3XD76
Secondary accession number(s): Q7DCA5, Q9Z9H2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 6, 2013
Last sequence update: November 16, 2011
Last modified: January 20, 2016
This is version 33 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.