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P56220

- DAPD_UNKP

UniProt

P56220 - DAPD_UNKP

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Protein
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Gene
dapD
Organism
Unknown prokaryotic organism
Status
Reviewed - Annotation score: 4 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

Enzyme regulationi

Inhibited by p-(chloromercuri)benzenesulfonic acid and cobalt.1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei104 – 1041Substrate
Binding sitei141 – 1411Substrate

GO - Molecular functioni

  1. 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. diaminopimelate biosynthetic process Source: UniProtKB-HAMAP
  2. lysine biosynthetic process via diaminopimelate Source: UniProtKB-HAMAP
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-succinyltransferase (EC:2.3.1.117)
Alternative name(s):
Tetrahydrodipicolinate N-succinyltransferase
Short name:
THDP succinyltransferase
Short name:
THP succinyltransferase
Short name:
Tetrahydropicolinate succinylase
Gene namesi
Name:dapD
OrganismiUnknown prokaryotic organism
Taxonomic identifieri2725 [NCBI]
Taxonomic lineageiBacteriaenvironmental samples

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 2742742,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferaseUniRule annotation
PRO_0000196949Add
BLAST

Interactioni

Subunit structurei

Homotrimer.1 Publication

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi2 – 1312
Helixi14 – 174
Turni20 – 223
Helixi25 – 3915
Beta strandi45 – 495
Beta strandi52 – 554
Helixi57 – 6913
Beta strandi73 – 764
Beta strandi78 – 869
Helixi89 – 924
Helixi95 – 1017
Beta strandi110 – 1123
Beta strandi125 – 1284
Beta strandi144 – 1463
Turni168 – 1714
Beta strandi214 – 2163
Turni217 – 2193
Beta strandi221 – 2233
Beta strandi225 – 2273
Beta strandi231 – 2399
Beta strandi241 – 2444
Beta strandi246 – 25510
Helixi258 – 2647
Helixi268 – 2703

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1KGQX-ray2.00A1-274[»]
1KGTX-ray2.30A1-274[»]
1TDTX-ray2.20A/B/C1-259[»]
2TDTX-ray2.00A1-274[»]
3TDTX-ray2.00A1-274[»]
ProteinModelPortaliP56220.
SMRiP56220. Positions 1-274.

Miscellaneous databases

EvolutionaryTraceiP56220.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Repeat

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.

P56220-1 [UniParc]FASTAAdd to Basket

« Hide

MQQLQNVIES AFERRADITP ANVDTVTREA VNQVIGLLDS GALRVAEKID    50
GQWVTHQWLK KAVLLSFRIN DNKVMDGAET RYYDKVPMKF ADYDEARFQK 100
EGFRVVPPAT VRQGAFIARN TVLMPSYVNI GAYVDEGTMV DTWATVGSCA 150
QIGKNVHLSG GVGIGGVLEP LQANPTIIED NCFIGARSEV VEGVIVEEGS 200
VISMGVYLGQ STRIYDRETG EIHYGRVPAG SVVVSGNLPS KDGSYSLYCA 250
VIVKKVDAKT RGKVGINELL RTID 274
Length:274
Mass (Da):29,887
Last modified:December 15, 1998 - v2
Checksum:iB1F54AE159C13278
GO

Cross-referencesi

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1KGQ X-ray 2.00 A 1-274 [» ]
1KGT X-ray 2.30 A 1-274 [» ]
1TDT X-ray 2.20 A/B/C 1-259 [» ]
2TDT X-ray 2.00 A 1-274 [» ]
3TDT X-ray 2.00 A 1-274 [» ]
ProteinModelPortali P56220.
SMRi P56220. Positions 1-274.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00019 .

Miscellaneous databases

EvolutionaryTracei P56220.

Family and domain databases

Gene3Di 1.10.166.10. 1 hit.
HAMAPi MF_00811. DapD.
InterProi IPR005664. DapD_Trfase_Hexpep_rpt_fam.
IPR001451. Hexapep_transf.
IPR018357. Hexapep_transf_CS.
IPR023180. THP_succinylTrfase_dom1.
IPR011004. Trimer_LpxA-like.
[Graphical view ]
PANTHERi PTHR19136:SF52. PTHR19136:SF52. 1 hit.
Pfami PF00132. Hexapep. 1 hit.
PF14805. THDPS_N_2. 1 hit.
[Graphical view ]
SUPFAMi SSF51161. SSF51161. 1 hit.
TIGRFAMsi TIGR00965. dapD. 1 hit.
PROSITEi PS00101. HEXAPEP_TRANSFERASES. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Crystallization and preliminary crystallographic analysis of tetrahydrodipicolinate-N-succinyltransferase."
    Binder D.A., Blanchard J.S., Roderick S.L.
    Proteins 26:115-117(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CRYSTALLIZATION.
  2. "The three-dimensional structure of a mycobacterial DapD provides insights into DapD diversity and reveals unexpected particulars about the enzymatic mechanism."
    Schuldt L., Weyand S., Kefala G., Weiss M.S.
    J. Mol. Biol. 389:863-879(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISCUSSION OF ORIGIN OF SEQUENCE.
  3. "Three-dimensional structure of tetrahydrodipicolinate N-succinyltransferase."
    Beaman T.W., Binder D.A., Blanchard J.S., Roderick S.L.
    Biochemistry 36:489-494(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), ENZYME REGULATION, SUBUNIT.
  4. "The conformational change and active site structure of tetrahydrodipicolinate N-succinyltransferase."
    Beaman T.W., Blanchard J.S., Roderick S.L.
    Biochemistry 37:10363-10369(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEXES WITH ANALOGS SUBSTRATE.
  5. "Acyl group specificity at the active site of tetrahydrodipicolinate N-succinyltransferase."
    Beaman T.W., Vogel K.W., Drueckhammer D.G., Blanchard J.S., Roderick S.L.
    Protein Sci. 11:974-979(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEXES WITH ANALOGS SUBSTRATES.

Entry informationi

Entry nameiDAPD_UNKP
AccessioniPrimary (citable) accession number: P56220
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: December 15, 1998
Last modified: May 14, 2014
This is version 83 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

Was originally thought to originate from Mycobacterium bovis (1 Publication, 1 Publication, 1 Publication and 1 Publication). However, there is now convincing evidence that this is incorrect (1 Publication). The source is unknown, but the sequence similarity suggests the protein is of enterobacterial origin.

Keywords - Technical termi

3D-structure

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

External Data

Dasty 3

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