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Entry version 32 (18 Sep 2019)
Sequence version 1 (16 Apr 2014)
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Protein

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

Gene

dapD

Organism
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Catalyzes the conversion of the cyclic tetrahydrodipicolinate (THDP) into the acyclic N-succinyl-L-2-amino-6-oxopimelate using succinyl-CoA.1 Publication

Miscellaneous

Was identified as a high-confidence drug target.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

Is activated by Mg2+, Ca2+ and Mn2+, and inhibited by Zn2+ and Co2+. Is not inhibited by EDTA in vitro.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>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. Probable N-succinyldiaminopimelate aminotransferase DapC (dapC)
  3. Putative succinyl-diaminopimelate desuccinylase DapE (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
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi166Magnesium 1; shared with trimeric partners1 Publication1
Metal bindingi183Magnesium 2; shared with trimeric partners1 Publication1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei199Acyl-anhydride intermediate1 Publication1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei201Succinyl-CoA1 Publication1
Binding sitei216Succinyl-CoA; via amide nitrogen1 Publication1
Binding sitei219Succinyl-CoA1 Publication1
Binding sitei242Succinyl-CoA; via amide nitrogen1 Publication1
Binding sitei265Succinyl-CoA; via carbonyl oxygen1 Publication1
Binding sitei277Succinyl-CoA1 Publication1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

  • 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity Source: MTBBASE
  • coenzyme binding Source: MTBBASE
  • magnesium ion binding Source: MTBBASE
  • sodium ion binding Source: MTBBASE

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionAcyltransferase, Transferase
Biological processAmino-acid biosynthesis, Diaminopimelate biosynthesis, Lysine biosynthesis
LigandMagnesium, Metal-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
MTBH37RV:G185E-5371-MONOMER

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA00034;UER00019

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferaseUniRule annotation (EC:2.3.1.1171 Publication)
Alternative name(s):
Tetrahydrodipicolinate N-succinyltransferaseUniRule annotation
Short name:
THDP succinyltransferaseUniRule annotation
Short name:
THP succinyltransferaseUniRule annotation
Tetrahydropicolinate succinylaseUniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:dapDUniRule annotation
Ordered Locus Names:Rv1201c
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiMycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83332 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000001584 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

Organism-specific databases

Mycobacterium tuberculosis strain H37Rv genome database

More...
TubercuListi
Rv1201c

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi199E → A: Loss of activity. 1 Publication1
Mutagenesisi222G → P: Loss of activity. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00004122541 – 3172,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferaseAdd BLAST317

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P9WP21

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homotrimer.

1 Publication

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
83332.Rv1201c

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1317
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
P9WP21

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni257 – 258Succinyl-CoA binding1 Publication2
Regioni290 – 293Succinyl-CoA binding1 Publication4

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the type 2 tetrahydrodipicolinate N-succinyltransferase family.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105EJ3 Bacteria
COG2171 LUCA

KEGG Orthology (KO)

More...
KOi
K00674

Identification of Orthologs from Complete Genome Data

More...
OMAi
TVLDTWF

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P9WP21

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.60.70, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_02122 DapD_type2, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR019875 DapD_actinobacteria
IPR001451 Hexapep
IPR032784 THDPS_M
IPR038361 THDPS_M_sf
IPR011004 Trimer_LpxA-like_sf
IPR026586 Type2_DapD

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF14602 Hexapep_2, 1 hit
PF14789 THDPS_M, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF51161 SSF51161, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR03535 DapD_actino, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P9WP21-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSTVTGAAGI GLATLAADGS VLDTWFPAPE LTESGTSATS RLAVSDVPVE
60 70 80 90 100
LAALIGRDDD RRTETIAVRT VIGSLDDVAA DPYDAYLRLH LLSHRLVAPH
110 120 130 140 150
GLNAGGLFGV LTNVVWTNHG PCAIDGFEAV RARLRRRGPV TVYGVDKFPR
160 170 180 190 200
MVDYVVPTGV RIADADRVRL GAHLAPGTTV MHEGFVNYNA GTLGASMVEG
210 220 230 240 250
RISAGVVVGD GSDVGGGASI MGTLSGGGTH VISIGKRCLL GANSGLGISL
260 270 280 290 300
GDDCVVEAGL YVTAGTRVTM PDSNSVKARE LSGSSNLLFR RNSVSGAVEV
310
LARDGQGIAL NEDLHAN
Length:317
Mass (Da):32,642
Last modified:April 16, 2014 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iEF204F46B90ADFF3
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AL123456 Genomic DNA Translation: CCP43957.1

Protein sequence database of the Protein Information Resource

More...
PIRi
G70608

NCBI Reference Sequences

More...
RefSeqi
NP_215717.1, NC_000962.3
WP_003898768.1, NZ_NVQJ01000039.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
CCP43957; CCP43957; Rv1201c

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
886088

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
mtu:Rv1201c
mtv:RVBD_1201c

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|83332.111.peg.1342

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL123456 Genomic DNA Translation: CCP43957.1
PIRiG70608
RefSeqiNP_215717.1, NC_000962.3
WP_003898768.1, NZ_NVQJ01000039.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3FSXX-ray2.15A/B/C/D/E2-317[»]
3FSYX-ray1.97A/B/C/D/E2-317[»]
SMRiP9WP21
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi83332.Rv1201c

Proteomic databases

PaxDbiP9WP21

Genome annotation databases

EnsemblBacteriaiCCP43957; CCP43957; Rv1201c
GeneIDi886088
KEGGimtu:Rv1201c
mtv:RVBD_1201c
PATRICifig|83332.111.peg.1342

Organism-specific databases

TubercuListiRv1201c

Phylogenomic databases

eggNOGiENOG4105EJ3 Bacteria
COG2171 LUCA
KOiK00674
OMAiTVLDTWF
PhylomeDBiP9WP21

Enzyme and pathway databases

UniPathwayiUPA00034;UER00019
BioCyciMTBH37RV:G185E-5371-MONOMER

Family and domain databases

Gene3Di3.30.60.70, 1 hit
HAMAPiMF_02122 DapD_type2, 1 hit
InterProiView protein in InterPro
IPR019875 DapD_actinobacteria
IPR001451 Hexapep
IPR032784 THDPS_M
IPR038361 THDPS_M_sf
IPR011004 Trimer_LpxA-like_sf
IPR026586 Type2_DapD
PfamiView protein in Pfam
PF14602 Hexapep_2, 1 hit
PF14789 THDPS_M, 1 hit
SUPFAMiSSF51161 SSF51161, 1 hit
TIGRFAMsiTIGR03535 DapD_actino, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiDAPD_MYCTU
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P9WP21
Secondary accession number(s): L0T666, O05302, Q7D8M6
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 16, 2014
Last sequence update: April 16, 2014
Last modified: September 18, 2019
This is version 32 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh
    Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh: entries and gene names
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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