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Protein

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

Gene

dapD

Organism
Yersinia pestis
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

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

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), 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (dapD)
  2. 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
Binding sitei104SubstrateUniRule annotation1
Binding sitei141SubstrateUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Acyltransferase, Transferase

Keywords - Biological processi

Amino-acid biosynthesis, Diaminopimelate biosynthesis, Lysine biosynthesis

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
Short name:
Tetrahydropicolinate succinylaseUniRule annotation
Gene namesi
Name:dapDUniRule annotation
Ordered Locus Names:YPO1041, y3140, YP_2810
OrganismiYersinia pestis
Taxonomic identifieri632 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesYersiniaceaeYersinia
Proteomesi
  • UP000000815 Componenti: Chromosome
  • UP000001019 Componenti: Chromosome
  • UP000002490 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001969781 – 2742,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferaseAdd BLAST274

Interactioni

Subunit structurei

Homotrimer.UniRule annotation

Protein-protein interaction databases

IntActiQ8ZH69. 4 interactors.
STRINGi187410.y3140.

Structurei

Secondary structure

1274
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi1 – 13Combined sources13
Helixi15 – 17Combined sources3
Turni20 – 22Combined sources3
Helixi25 – 39Combined sources15
Beta strandi45 – 49Combined sources5
Beta strandi52 – 55Combined sources4
Helixi57 – 68Combined sources12
Beta strandi73 – 77Combined sources5
Beta strandi80 – 86Combined sources7
Turni89 – 92Combined sources4
Helixi95 – 101Combined sources7
Beta strandi110 – 112Combined sources3
Beta strandi125 – 128Combined sources4
Beta strandi144 – 146Combined sources3
Beta strandi214 – 216Combined sources3
Turni217 – 219Combined sources3
Beta strandi225 – 227Combined sources3
Beta strandi231 – 239Combined sources9
Beta strandi246 – 255Combined sources10
Helixi266 – 270Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3GOSX-ray1.80A/B/C1-274[»]
ProteinModelPortaliQ8ZH69.
SMRiQ8ZH69.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8ZH69.

Family & Domainsi

Sequence similaritiesi

Belongs to the transferase hexapeptide repeat family.UniRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiENOG4105DMJ. Bacteria.
COG2171. LUCA.
HOGENOMiHOG000003295.
KOiK00674.
OMAiWVKKAVV.

Family and domain databases

Gene3Di1.10.166.10. 1 hit.
HAMAPiMF_00811. DapD. 1 hit.
InterProiIPR005664. DapD_Trfase_Hexpep_rpt_fam.
IPR001451. Hexapep.
IPR018357. Hexapep_transf_CS.
IPR023180. THP_succinylTrfase_dom1.
IPR011004. Trimer_LpxA-like.
[Graphical view]
PANTHERiPTHR19136:SF52. PTHR19136:SF52. 1 hit.
PfamiPF00132. Hexapep. 1 hit.
PF14602. Hexapep_2. 1 hit.
PF14805. THDPS_N_2. 1 hit.
[Graphical view]
SUPFAMiSSF51161. SSF51161. 1 hit.
TIGRFAMsiTIGR00965. dapD. 1 hit.
PROSITEiPS00101. HEXAPEP_TRANSFERASES. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8ZH69-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQQLQNVIET AFERRADITP ANVDTVTREA ITHVIDLLDT GALRVAEKID
60 70 80 90 100
GQWVTHQWLK KAVLLSFRIN DNQVMEGAET RYYDKVPMKF AGYDEARFQR
110 120 130 140 150
EGFRVVPPAT VRKGAFIARN TVLMPSYVNI GAFVDEGTMV DTWATVGSCA
160 170 180 190 200
QIGKNVHLSG GVGIGGVLEP LQANPTIIED NCFVGARSEV VEGVIVEEGS
210 220 230 240 250
VISMGVFIGQ STRIYDRETG EVHYGRVPAG SVVVSGNLPS KDGSYSLYCA
260 270
VIVKKVDAKT RSKVGINELL RTID
Length:274
Mass (Da):29,937
Last modified:March 1, 2002 - v1
Checksum:i5BA5F77C11D66282
GO

Sequence cautioni

The sequence AAM86690 differs from that shown. Reason: Erroneous initiation.Curated
The sequence AAS62994 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL19706.1.
AE009952 Genomic DNA. Translation: AAM86690.1. Different initiation.
AE017042 Genomic DNA. Translation: AAS62994.1. Different initiation.
PIRiAH0127.
RefSeqiWP_002212128.1. NZ_LQBA01000041.1.
YP_002346084.1. NC_003143.1.

Genome annotation databases

EnsemblBacteriaiAAM86690; AAM86690; y3140.
AAS62994; AAS62994; YP_2810.
GeneIDi1173881.
KEGGiype:YPO1041.
ypk:y3140.
ypm:YP_2810.
PATRICi18591335. VBIYerPes7843_1401.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL19706.1.
AE009952 Genomic DNA. Translation: AAM86690.1. Different initiation.
AE017042 Genomic DNA. Translation: AAS62994.1. Different initiation.
PIRiAH0127.
RefSeqiWP_002212128.1. NZ_LQBA01000041.1.
YP_002346084.1. NC_003143.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3GOSX-ray1.80A/B/C1-274[»]
ProteinModelPortaliQ8ZH69.
SMRiQ8ZH69.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ8ZH69. 4 interactors.
STRINGi187410.y3140.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAM86690; AAM86690; y3140.
AAS62994; AAS62994; YP_2810.
GeneIDi1173881.
KEGGiype:YPO1041.
ypk:y3140.
ypm:YP_2810.
PATRICi18591335. VBIYerPes7843_1401.

Phylogenomic databases

eggNOGiENOG4105DMJ. Bacteria.
COG2171. LUCA.
HOGENOMiHOG000003295.
KOiK00674.
OMAiWVKKAVV.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00019.

Miscellaneous databases

EvolutionaryTraceiQ8ZH69.

Family and domain databases

Gene3Di1.10.166.10. 1 hit.
HAMAPiMF_00811. DapD. 1 hit.
InterProiIPR005664. DapD_Trfase_Hexpep_rpt_fam.
IPR001451. Hexapep.
IPR018357. Hexapep_transf_CS.
IPR023180. THP_succinylTrfase_dom1.
IPR011004. Trimer_LpxA-like.
[Graphical view]
PANTHERiPTHR19136:SF52. PTHR19136:SF52. 1 hit.
PfamiPF00132. Hexapep. 1 hit.
PF14602. Hexapep_2. 1 hit.
PF14805. THDPS_N_2. 1 hit.
[Graphical view]
SUPFAMiSSF51161. SSF51161. 1 hit.
TIGRFAMsiTIGR00965. dapD. 1 hit.
PROSITEiPS00101. HEXAPEP_TRANSFERASES. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDAPD_YERPE
AccessioniPrimary (citable) accession number: Q8ZH69
Secondary accession number(s): Q0WI04, Q74S45, Q8CZY9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2005
Last sequence update: March 1, 2002
Last modified: November 2, 2016
This is version 103 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.