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Protein

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

Gene

dapD

Organism
Brucella suis biovar 1 (strain 1330)
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

Pathway: 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
Binding sitei111 – 1111SubstrateUniRule annotation
Binding sitei148 – 1481SubstrateUniRule annotation

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:BRA1028, BS1330_II1020
OrganismiBrucella suis biovar 1 (strain 1330)
Taxonomic identifieri204722 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBrucellaceaeBrucella
ProteomesiUP000007104 Componenti: Chromosome II

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 – 2842842,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferasePRO_0000196922Add
BLAST

Proteomic databases

PRIDEiQ8FV25.

Interactioni

Subunit structurei

Homotrimer.UniRule annotation

Structurei

Secondary structure

1
284
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi7 – 1812Combined sources
Helixi19 – 224Combined sources
Helixi29 – 4315Combined sources
Beta strandi49 – 524Combined sources
Beta strandi58 – 603Combined sources
Helixi62 – 7413Combined sources
Beta strandi78 – 814Combined sources
Helixi84 – 863Combined sources
Beta strandi88 – 925Combined sources
Turni96 – 994Combined sources
Helixi102 – 1087Combined sources
Beta strandi117 – 1193Combined sources
Beta strandi132 – 1354Combined sources
Beta strandi151 – 1533Combined sources
Beta strandi221 – 2233Combined sources
Turni224 – 2263Combined sources
Beta strandi232 – 2343Combined sources
Beta strandi238 – 2469Combined sources
Beta strandi258 – 26710Combined sources
Helixi270 – 2756Combined sources
Helixi278 – 2836Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3EG4X-ray1.87A1-284[»]
ProteinModelPortaliQ8FV25.
SMRiQ8FV25. Positions 6-283.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8FV25.

Family & Domainsi

Sequence similaritiesi

Belongs to the transferase hexapeptide repeat family.UniRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG2171.
HOGENOMiHOG000003295.
KOiK00674.
OMAiQVPCALI.
OrthoDBiEOG68H8BV.

Family and domain databases

Gene3Di1.10.166.10. 1 hit.
HAMAPiMF_00811. DapD.
InterProiIPR005664. DapD_Trfase_Hexpep_rpt_fam.
IPR001451. Hexapep_transf.
IPR018357. Hexapep_transf_CS.
IPR023180. THP_succinylTrfase_dom1.
IPR011004. Trimer_LpxA-like.
[Graphical view]
PANTHERiPTHR19136:SF52. PTHR19136:SF52. 1 hit.
PfamiPF00132. Hexapep. 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.

Q8FV25-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKPDLASLE KTIEKAFDER DGINTATRGE VREAVEQSLI LLDRGEVRVA
60 70 80 90 100
EKQADGNWHV NQWLKKAVLL SFRLNPMEVI KGGPGQSSWW DKVPSKFDGW
110 120 130 140 150
TANEFEKAGF RAVPNCIVRH SAYIAPNAIL MPSFVNLGAY VDKGAMIDTW
160 170 180 190 200
ATVGSCAQIG KNVHLSGGVG IGGVLEPMQA GPTIIEDNCF IGARSEVVEG
210 220 230 240 250
CIVREGSVLG MGVFIGKSTK IVDRATGEVF YGEVPPYSVV VAGTMPGKNV
260 270 280
PGENWGPSLY CAVIVKRADE KTRSKTSINE LLRD
Length:284
Mass (Da):30,753
Last modified:March 1, 2003 - v1
Checksum:i9EF76F51038A6350
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014292 Genomic DNA. Translation: AAN34196.1.
CP002998 Genomic DNA. Translation: AEM20472.1.
PIRiAD3543.
RefSeqiNP_700191.1. NC_004311.2.
WP_002965622.1. NZ_KN046805.1.
YP_005614698.1. NC_017250.1.

Genome annotation databases

EnsemblBacteriaiAAN34196; AAN34196; BRA1028.
AEM20472; AEM20472; BS1330_II1020.
GeneIDi3828144.
KEGGibms:BRA1028.
bsi:BS1330_II1020.
PATRICi17794891. VBIBruSui107850_3253.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014292 Genomic DNA. Translation: AAN34196.1.
CP002998 Genomic DNA. Translation: AEM20472.1.
PIRiAD3543.
RefSeqiNP_700191.1. NC_004311.2.
WP_002965622.1. NZ_KN046805.1.
YP_005614698.1. NC_017250.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3EG4X-ray1.87A1-284[»]
ProteinModelPortaliQ8FV25.
SMRiQ8FV25. Positions 6-283.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiQ8FV25.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAN34196; AAN34196; BRA1028.
AEM20472; AEM20472; BS1330_II1020.
GeneIDi3828144.
KEGGibms:BRA1028.
bsi:BS1330_II1020.
PATRICi17794891. VBIBruSui107850_3253.

Phylogenomic databases

eggNOGiCOG2171.
HOGENOMiHOG000003295.
KOiK00674.
OMAiQVPCALI.
OrthoDBiEOG68H8BV.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00019.

Miscellaneous databases

EvolutionaryTraceiQ8FV25.

Family and domain databases

Gene3Di1.10.166.10. 1 hit.
HAMAPiMF_00811. DapD.
InterProiIPR005664. DapD_Trfase_Hexpep_rpt_fam.
IPR001451. Hexapep_transf.
IPR018357. Hexapep_transf_CS.
IPR023180. THP_succinylTrfase_dom1.
IPR011004. Trimer_LpxA-like.
[Graphical view]
PANTHERiPTHR19136:SF52. PTHR19136:SF52. 1 hit.
PfamiPF00132. Hexapep. 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...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 1330.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 1330.
  3. "Crystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate n-succinyltransferase from Brucella melitensis biovar abortus 2308."
    Seattle structural genomics center for infectious disease (SSGCID)
    Submitted (SEP-2008) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.89 ANGSTROMS).

Entry informationi

Entry nameiDAPD_BRUSU
AccessioniPrimary (citable) accession number: Q8FV25
Secondary accession number(s): G0KE34
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2005
Last sequence update: March 1, 2003
Last modified: June 24, 2015
This is version 84 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

Documents

  1. Brucella suis
    Brucella suis (strain 1330): entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.