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UniProtKB - P23970 (MEND_BACSU)

Entry version 142 (12 Aug 2020)
Sequence version 3 (15 Jul 1999)
Previous versions | rss
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Protein

2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

Gene

menD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score:

Annotation score:3 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 thiamine diphosphate-dependent decarboxylation of 2-oxoglutarate and the subsequent addition of the resulting succinic semialdehyde-thiamine pyrophosphate anion to isochorismate to yield 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC).UniRule annotation

Caution

Used to include what was called 'MenCF'.Curated

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Protein has several cofactor binding sites:

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: 1,4-dihydroxy-2-naphthoate biosynthesis

This protein is involved in step 2 of the subpathway that synthesizes 1,4-dihydroxy-2-naphthoate from chorismate.UniRule annotation
Proteins known to be involved in the 7 steps of the subpathway in this organism are:
  1. Isochorismate synthase MenF (menF)
  2. 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (menD)
  3. Putative 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (menH)
  4. o-succinylbenzoate synthase (menC)
  5. 2-succinylbenzoate--CoA ligase (menE)
  6. 1,4-dihydroxy-2-naphthoyl-CoA synthase (menB)
  7. no protein annotated in this organism
This subpathway is part of the pathway 1,4-dihydroxy-2-naphthoate biosynthesis, which is itself part of Quinol/quinone metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 1,4-dihydroxy-2-naphthoate from chorismate, the pathway 1,4-dihydroxy-2-naphthoate biosynthesis and in Quinol/quinone metabolism.

Pathwayi: menaquinone biosynthesis

This protein is involved in the pathway menaquinone biosynthesis, which is part of Quinol/quinone metabolism.UniRule annotation
View all proteins of this organism that are known to be involved in the pathway menaquinone biosynthesis and in Quinol/quinone metabolism.

<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

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<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 functionTransferase
Biological processMenaquinone biosynthesis
LigandMagnesium, Manganese, Metal-binding, Thiamine pyrophosphate

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		BSUB:BSU30820-MONOMER
MetaCyc:MONOMER-13808

BRENDA Comprehensive Enzyme Information System

More...BRENDAi		2.2.1.9, 658

SABIO-RK: Biochemical Reaction Kinetics Database

More...SABIO-RKi		P23970

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

More...UniPathwayi		UPA00079
UPA01057;UER00164

<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%5Fand%5Ftaxonomy%5Fsection">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-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthaseUniRule annotation (EC:2.2.1.9UniRule annotation)
Short name:
SEPHCHC synthaseUniRule annotation
Alternative name(s):
Menaquinone biosynthesis protein MenDUniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:menDUniRule annotation
Ordered Locus Names:BSU30820
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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>OrganismiBacillus subtilis (strain 168)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 identifieri224308 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 lineageiBacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
  • UP000001570 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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

<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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000908281 – 5802-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthaseAdd BLAST580

Proteomic databases

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

More...PaxDbi		P23970

PRoteomics IDEntifications database

More...PRIDEi		P23970

<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%5Fsection">'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%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer.

UniRule annotation

Protein-protein interaction databases

STRING: functional protein association networks

More...STRINGi		224308.BSU30820

<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

1580
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

More...SMRi		P23970

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...EvolutionaryTracei		P23970

<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

<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 TPP enzyme family. MenD subfamily.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG1165, Bacteria

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P23970

KEGG Orthology (KO)

More...KOi		K02551

Identification of Orthologs from Complete Genome Data

More...OMAi		HDTNGFL

Database for complete collections of gene phylogenies

More...PhylomeDBi		P23970

Family and domain databases

HAMAP database of protein families

More...HAMAPi		MF_01659, MenD, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR029035, DHS-like_NAD/FAD-binding_dom
IPR004433, MenaQ_synth_MenD
IPR032264, MenD_middle
IPR029061, THDP-binding
IPR012001, Thiamin_PyroP_enz_TPP-bd_dom
IPR011766, TPP_enzyme-bd_C

The PANTHER Classification System

More...PANTHERi		PTHR42916, PTHR42916, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF02775, TPP_enzyme_C, 1 hit
PF16582, TPP_enzyme_M_2, 1 hit
PF02776, TPP_enzyme_N, 1 hit

PIRSF; a whole-protein classification database

More...PIRSFi		PIRSF004983, MenD, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF52467, SSF52467, 1 hit
SSF52518, SSF52518, 2 hits

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR00173, menD, 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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

P23970-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTVNPITHYI GSFIDEFALS GITDAVVCPG SRSTPLAVLC AAHPDISVHV 
        60         70         80         90        100
QIDERSAGFF ALGLAKAKQR PVLLICTSGT AAANFYPAVV EAHYSRVPII 
       110        120        130        140        150
VLTADRPHEL REVGAPQAIN QHFLFGNFVK FFTDSALPEE SPQMLRYIRT 
       160        170        180        190        200
LASRAAGEAQ KRPMGPVHVN VPLREPLMPD LSDEPFGRMR TGRHVSVKTG 
       210        220        230        240        250
TQSVDRESLS DVAEMLAEAE KGMIVCGELH SDADKENIIA LSKALQYPIL 
       260        270        280        290        300
ADPLSNLRNG VHDKSTVIDA YDSFLKDDEL KRKLRPDVVI RFGPMPVSKP 
       310        320        330        340        350
VFLWLKDDPT IQQIVIDEDG GWRDPTQASA HMIHCNASVF AEEIMAGLTA 
       360        370        380        390        400
ATRSSEWLEK WQFVNGRFRE HLQTISSEDV SFEGNLYRIL QHLVPENSSL 
       410        420        430        440        450
FVGNSMPIRD VDTFFEKQDR PFRIYSNRGA NGIDGVVSSA MGVCEGTKAP 
       460        470        480        490        500
VTLVIGDLSF YHDLNGLLAA KKLGIPLTVI LVNNDGGGIF SFLPQASEKT 
       510        520        530        540        550
HFEDLFGTPT GLDFKHAAAL YGGTYSCPAS WDEFKTAYAP QADKPGLHLI 
       560        570        580
EIKTDRQSRV QLHRDMLNEA VREVKKQWEL
Length:580
Mass (Da):64,092
Last modified:July 15, 1999 - v3
<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:i3B416F8DA18FFAF2
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti112E → R in AAA50398 (PubMed:8566759).Curated1
Sequence conflicti112E → R in AAC37014 (PubMed:8566759).Curated1
Sequence conflicti152A → P in AAC37014 (PubMed:8566759).Curated1
Sequence conflicti540 – 580PQADK…KQWEL → RRQTSPDSI in AAA50399 (PubMed:8566759).CuratedAdd BLAST41
Sequence conflicti540 – 580PQADK…KQWEL → RRQTSPDSI in AAC37014 (PubMed:8566759).CuratedAdd BLAST41

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
M74521 Genomic DNA Translation: AAA50398.1 Sequence problems.
M74521 Genomic DNA Translation: AAA50399.1 Sequence problems.
M74538 Genomic DNA Translation: AAC37014.1
AF008220 Genomic DNA Translation: AAC00224.1
AL009126 Genomic DNA Translation: CAB15060.1

Protein sequence database of the Protein Information Resource

More...PIRi		G69656

NCBI Reference Sequences

More...RefSeqi		NP_390960.1, NC_000964.3
WP_003229050.1, NZ_JNCM01000036.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		CAB15060; CAB15060; BSU30820

Database of genes from NCBI RefSeq genomes

More...GeneIDi		937198

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		bsu:BSU30820

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|224308.179.peg.3340

<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
M74521 Genomic DNA Translation: AAA50398.1 Sequence problems.
M74521 Genomic DNA Translation: AAA50399.1 Sequence problems.
M74538 Genomic DNA Translation: AAC37014.1
AF008220 Genomic DNA Translation: AAC00224.1
AL009126 Genomic DNA Translation: CAB15060.1
PIRiG69656
RefSeqiNP_390960.1, NC_000964.3
WP_003229050.1, NZ_JNCM01000036.1

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
2X7JX-ray2.35A/B/C/D1-580[»]
SMRiP23970
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi224308.BSU30820

Proteomic databases

PaxDbiP23970
PRIDEiP23970

Genome annotation databases

EnsemblBacteriaiCAB15060; CAB15060; BSU30820
GeneIDi937198
KEGGibsu:BSU30820
PATRICifig|224308.179.peg.3340

Phylogenomic databases

eggNOGiCOG1165, Bacteria
InParanoidiP23970
KOiK02551
OMAiHDTNGFL
PhylomeDBiP23970

Enzyme and pathway databases

UniPathwayiUPA00079
UPA01057;UER00164
BioCyciBSUB:BSU30820-MONOMER
MetaCyc:MONOMER-13808
BRENDAi2.2.1.9, 658
SABIO-RKiP23970

Miscellaneous databases

EvolutionaryTraceiP23970

Family and domain databases

HAMAPiMF_01659, MenD, 1 hit
InterProiView protein in InterPro
IPR029035, DHS-like_NAD/FAD-binding_dom
IPR004433, MenaQ_synth_MenD
IPR032264, MenD_middle
IPR029061, THDP-binding
IPR012001, Thiamin_PyroP_enz_TPP-bd_dom
IPR011766, TPP_enzyme-bd_C
PANTHERiPTHR42916, PTHR42916, 1 hit
PfamiView protein in Pfam
PF02775, TPP_enzyme_C, 1 hit
PF16582, TPP_enzyme_M_2, 1 hit
PF02776, TPP_enzyme_N, 1 hit
PIRSFiPIRSF004983, MenD, 1 hit
SUPFAMiSSF52467, SSF52467, 1 hit
SSF52518, SSF52518, 2 hits
TIGRFAMsiTIGR00173, menD, 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 nameiMEND_BACSU
<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: P23970
Secondary accession number(s): O34492, P23969
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: July 15, 1999
Last modified: August 12, 2020
This is version 142 of the entry and version 3 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, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  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
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