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P56220 (DAPD_UNKP) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 83. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:dapD
OrganismUnknown prokaryotic organism
Taxonomic identifier2725 [NCBI]
Taxonomic lineageBacteriaenvironmental samples

Protein attributes

Sequence length274 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Catalytic activity

Succinyl-CoA + (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + H2O = CoA + N-succinyl-L-2-amino-6-oxoheptanedioate. HAMAP-Rule MF_00811

Enzyme regulation

Inhibited by p-(chloromercuri)benzenesulfonic acid and cobalt. Ref.3

Pathway

Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (succinylase route): step 1/3. HAMAP-Rule MF_00811

Subunit structure

Homotrimer. Ref.3

Subcellular location

Cytoplasm HAMAP-Rule MF_00811.

Sequence similarities

Belongs to the transferase hexapeptide repeat family.

Caution

Was originally thought to originate from Mycobacterium bovis (Ref.1, Ref.3, Ref.4 and Ref.5). However, there is now convincing evidence that this is incorrect (Ref.2). The source is unknown, but the sequence similarity suggests the protein is of enterobacterial origin.

Ontologies

Keywords
   Biological processAmino-acid biosynthesis
Diaminopimelate biosynthesis
Lysine biosynthesis
   Cellular componentCytoplasm
   DomainRepeat
   Molecular functionAcyltransferase
Transferase
   Technical term3D-structure
Gene Ontology (GO)
   Biological_processdiaminopimelate biosynthetic process

Inferred from electronic annotation. Source: UniProtKB-HAMAP

lysine biosynthetic process via diaminopimelate

Inferred from electronic annotation. Source: UniProtKB-HAMAP

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_function2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 2742742,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase HAMAP-Rule MF_00811
PRO_0000196949

Sites

Binding site1041Substrate
Binding site1411Substrate

Secondary structure

............................................... 274
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P56220 [UniParc].

Last modified December 15, 1998. Version 2.
Checksum: B1F54AE159C13278

FASTA27429,887
        10         20         30         40         50         60 
MQQLQNVIES AFERRADITP ANVDTVTREA VNQVIGLLDS GALRVAEKID GQWVTHQWLK 

        70         80         90        100        110        120 
KAVLLSFRIN DNKVMDGAET RYYDKVPMKF ADYDEARFQK EGFRVVPPAT VRQGAFIARN 

       130        140        150        160        170        180 
TVLMPSYVNI GAYVDEGTMV DTWATVGSCA QIGKNVHLSG GVGIGGVLEP LQANPTIIED 

       190        200        210        220        230        240 
NCFIGARSEV VEGVIVEEGS VISMGVYLGQ STRIYDRETG EIHYGRVPAG SVVVSGNLPS 

       250        260        270 
KDGSYSLYCA VIVKKVDAKT RGKVGINELL RTID 

« Hide

References

[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.

Cross-references

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
ProteinModelPortalP56220.
SMRP56220. Positions 1-274.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayUPA00034; UER00019.

Family and domain databases

Gene3D1.10.166.10. 1 hit.
HAMAPMF_00811. DapD.
InterProIPR005664. DapD_Trfase_Hexpep_rpt_fam.
IPR001451. Hexapep_transf.
IPR018357. Hexapep_transf_CS.
IPR023180. THP_succinylTrfase_dom1.
IPR011004. Trimer_LpxA-like.
[Graphical view]
PANTHERPTHR19136:SF52. PTHR19136:SF52. 1 hit.
PfamPF00132. Hexapep. 1 hit.
PF14805. THDPS_N_2. 1 hit.
[Graphical view]
SUPFAMSSF51161. SSF51161. 1 hit.
TIGRFAMsTIGR00965. dapD. 1 hit.
PROSITEPS00101. HEXAPEP_TRANSFERASES. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP56220.

Entry information

Entry nameDAPD_UNKP
AccessionPrimary (citable) accession number: P56220
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways