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

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P56220 (DAPD_UNKP) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 79. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

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 names

Name:

dapD

Organism

Unknown prokaryotic organism

Taxonomic identifier

2725 [NCBI]

Taxonomic lineage

Bacteria › environmental samples

Protein attributes

Sequence length	274 AA.
Sequence status	Complete.
Protein existence	Evidence 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 process	Amino-acid biosynthesis Diaminopimelate biosynthesis Lysine biosynthesis
Cellular component	Cytoplasm
Domain	Repeat
Molecular function	Acyltransferase Transferase
Technical term	3D-structure
Gene Ontology (GO)
Biological_process	diaminopimelate biosynthetic process Inferred from electronic annotation. Source: HAMAP lysine biosynthetic process via diaminopimelate Inferred from electronic annotation. Source: HAMAP
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 274

274

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase HAMAP-Rule MF_00811

PRO_0000196949

Sites

Binding site

104

Substrate

Binding site

141

Substrate

Secondary structure

274

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P56220 [UniParc].

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

274

29,887

        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

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	[»]

ProteinModelPortal

P56220.

SMR

P56220. Positions 1-274.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

UniPathway

UPA00034; UER00019.

Family and domain databases

Gene3D

1.10.166.10. 1 hit.

HAMAP

MF_00811. DapD.

InterPro

IPR005664. DapD_Trfase_Hexpep_rpt_fam.
IPR001451. Hexapep_transf.
IPR018357. Hexapep_transf_CS.
IPR023180. THP_succinylTrfase_dom1.
IPR011004. Trimer_LpxA-like.
[Graphical view]

PANTHER

PTHR19136:SF52. PTHR19136:SF52. 1 hit.

Pfam

PF00132. Hexapep. 2 hits.
[Graphical view]

SUPFAM

SSF51161. Trimer_LpxA_like. 1 hit.

TIGRFAMs

TIGR00965. dapD. 1 hit.

PROSITE

PS00101. HEXAPEP_TRANSFERASES. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P56220.

Entry information

Entry name

DAPD_UNKP

Accession

Primary (citable) accession number: P56220

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1998
Last sequence update:	December 15, 1998
Last modified:	April 3, 2013
This is version 79 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Secondary structure

Sequences

References

Cross-references

3D structure databases

Protocols and materials databases

Enzyme and pathway databases

Family and domain databases

Other

Entry information

Relevant documents