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Entry version 85 (12 Aug 2020)
Sequence version 1 (15 May 2007)
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Protein

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

Gene

menD

Organism
Chlorobium phaeovibrioides (strain DSM 265 / 1930) (Prosthecochloris vibrioformis (strain DSM 265))
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>
-Protein inferred from homologyi <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

<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. no protein annotated in this organism
  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

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

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
CPHA290318:G1G8E-411-MONOMER

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:Cvib_0397
<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>OrganismiChlorobium phaeovibrioides (strain DSM 265 / 1930) (Prosthecochloris vibrioformis (strain DSM 265))
<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 identifieri290318 [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 lineageiBacteriaChlorobiChlorobiaChlorobialesChlorobiaceaeChlorobium/Pelodictyon groupChlorobium
<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
  • UP000006700 <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_00003418101 – 5832-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthaseAdd BLAST583

<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
290318.Cvib_0397

<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

3D structure databases

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

More...
SMRi
A4SD60

Database of comparative protein structure models

More...
ModBasei
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

<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

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_006051_3_0_10

KEGG Orthology (KO)

More...
KOi
K02551

Identification of Orthologs from Complete Genome Data

More...
OMAi
HDTNGFL

Database of Orthologous Groups

More...
OrthoDBi
897995at2

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
IPR006189, CHASE_dom
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.

A4SD60-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MNNPQLTTVW SSVMVEELIR QGASFFCISP GSRSTPLTAA IARNPEASWK
60 70 80 90 100
MFPDERSAGF FALGHARATG FPAVLVCTSG TAVANYLPAV VEASNDRIPM
110 120 130 140 150
LILSADRPFE LRECGANQTI RQNGIFGTFT RWQMELPEPS TSIPLQSLLS
160 170 180 190 200
TIAHGVEKSL NSPRGPVHLN QPFREPFEPE SCSTPEPWLE PLQAWQTGRR
210 220 230 240 250
PSTVAAQPEK HPDMDSMRTL RELTGNARQP LIIAGNSTDE NDSHAIAELA
260 270 280 290 300
DDLQVPLYAD MTSGLRFSSS ILPWQQAFAS PEFRNAFRPD LVIHFGGGLI
310 320 330 340 350
SRHPSDALKQ WKPDHLAVIR NHPGRYSPDH SVTLSIEASL RLTADALRGC
360 370 380 390 400
RTGASALMAP AKRFFTEADR EIAAATAPDL PVSEIGTARI VSELLPPDHL
410 420 430 440 450
LFLSNSMPVR AMDSYAHTGK ENPIKTGTNR GASGIDGIIS TAAGFAEGHG
460 470 480 490 500
QPLCLMIGDL AFLHDLNALS LINSLRVPIQ LILLNNNGGG IFSFLPVSEF
510 520 530 540 550
DDIFEPNFAT PQNFSGRPAA AMFGLDYTAP LTNSEFRESL LSALNSNRST
560 570 580
IIEVVCSRSE NVRLHRALQA RLGLLATEAF FIP
Length:583
Mass (Da):63,450
Last modified:May 15, 2007 - 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:i43877A9013C42C62
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
CP000607 Genomic DNA Translation: ABP36419.1

NCBI Reference Sequences

More...
RefSeqi
WP_011889648.1, NC_009337.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
ABP36419; ABP36419; Cvib_0397

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
pvi:Cvib_0397

<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
CP000607 Genomic DNA Translation: ABP36419.1
RefSeqiWP_011889648.1, NC_009337.1

3D structure databases

SMRiA4SD60
ModBaseiSearch...

Protein-protein interaction databases

STRINGi290318.Cvib_0397

Genome annotation databases

EnsemblBacteriaiABP36419; ABP36419; Cvib_0397
KEGGipvi:Cvib_0397

Phylogenomic databases

eggNOGiCOG1165, Bacteria
HOGENOMiCLU_006051_3_0_10
KOiK02551
OMAiHDTNGFL
OrthoDBi897995at2

Enzyme and pathway databases

UniPathwayiUPA00079
UPA01057;UER00164
BioCyciCPHA290318:G1G8E-411-MONOMER

Family and domain databases

HAMAPiMF_01659, MenD, 1 hit
InterProiView protein in InterPro
IPR006189, CHASE_dom
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_CHLPM
<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: A4SD60
<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: July 1, 2008
Last sequence update: May 15, 2007
Last modified: August 12, 2020
This is version 85 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

Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families
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