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Protein

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

Gene

dapD

Organism
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Status
Reviewed-Annotation score: -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)DescriptionActionsGraphical viewLength
Metal bindingi205Magnesium; shared with trimeric partnersUniRule annotation1
Active sitei221Acyl-anhydride intermediateUniRule annotation1
Binding sitei223Succinyl-CoA1 Publication1
Binding sitei238Succinyl-CoA; via amide nitrogen1 Publication1
Binding sitei241Succinyl-CoA1 Publication1
Binding sitei264Succinyl-CoA; via amide nitrogen1 Publication1
Binding sitei304Succinyl-CoA1 Publication1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionAcyltransferase, Transferase
Biological processAmino-acid biosynthesis, Diaminopimelate biosynthesis, Lysine biosynthesis
LigandMagnesium, Metal-binding

Enzyme and pathway databases

BioCyciPAER208964:G1FZ6-3736-MONOMER
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 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Taxonomic identifieri208964 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
Proteomesi
  • UP000002438 Componenti: Chromosome

Organism-specific databases

PseudoCAPiPA3666

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004213011 – 3442,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferaseAdd BLAST344

Proteomic databases

PaxDbiG3XD76
PRIDEiG3XD76

2D gel databases

World-2DPAGEi0008:Q9Z9H2

Interactioni

Subunit structurei

Homotrimer.1 Publication

Protein-protein interaction databases

STRINGi208964.PA3666

Structurei

Secondary structure

1344
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi6 – 15Combined sources10
Beta strandi21 – 28Combined sources8
Beta strandi30 – 32Combined sources3
Helixi35 – 45Combined sources11
Beta strandi49 – 56Combined sources8
Helixi58 – 68Combined sources11
Turni69 – 71Combined sources3
Helixi73 – 83Combined sources11
Beta strandi89 – 96Combined sources8
Helixi103 – 114Combined sources12
Helixi128 – 131Combined sources4
Beta strandi135 – 138Combined sources4
Beta strandi141 – 144Combined sources4
Helixi145 – 157Combined sources13
Beta strandi164 – 170Combined sources7
Helixi173 – 175Combined sources3
Beta strandi182 – 186Combined sources5
Helixi187 – 189Combined sources3
Beta strandi194 – 196Combined sources3
Beta strandi200 – 202Combined sources3
Beta strandi212 – 220Combined sources9
Beta strandi222 – 224Combined sources3
Beta strandi234 – 236Combined sources3
Beta strandi267 – 270Combined sources4
Beta strandi289 – 293Combined sources5
Beta strandi299 – 304Combined sources6
Helixi305 – 308Combined sources4
Beta strandi315 – 318Combined sources4
Turni320 – 322Combined sources3
Beta strandi325 – 328Combined sources4
Helixi333 – 341Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni279 – 280Succinyl-CoA binding1 Publication2
Regioni287 – 289Succinyl-CoA binding1 Publication3
Regioni317 – 320Succinyl-CoA binding1 Publication4

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105EJ3 Bacteria
COG2171 LUCA
InParanoidiG3XD76
KOiK00674
OMAiTVLDTWF
PhylomeDBiG3XD76

Family and domain databases

Gene3Di3.30.60.70, 1 hit
HAMAPiMF_02122 DapD_type2, 1 hit
InterProiView protein in InterPro
IPR019876 DapD_gammaproteobac
IPR001451 Hexapep
IPR032784 THDPS_M
IPR038361 THDPS_M_sf
IPR011004 Trimer_LpxA-like_sf
IPR026586 Type2_DapD
PfamiView protein in Pfam
PF14602 Hexapep_2, 1 hit
PF14789 THDPS_M, 1 hit
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, NC_002516.2

Genome annotation databases

EnsemblBacteriaiAAG07054; AAG07054; PA3666
GeneIDi880584
KEGGipae:PA3666
PATRICifig|208964.12.peg.3835

Similar proteinsi

Entry informationi

Entry nameiDAPD_PSEAE
AccessioniPrimary (citable) accession number: G3XD76
Secondary accession number(s): Q7DCA5, Q9Z9H2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 6, 2013
Last sequence update: November 16, 2011
Last modified: March 28, 2018
This is version 43 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome
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Main funding by: National Institutes of Health