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Protein

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

Gene

menD

Organism
Rhodococcus jostii (strain RHA1)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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

Catalytic activityi

Isochorismate + 2-oxoglutarate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2.UniRule annotation

Cofactori

Protein has several cofactor binding sites:
  • Mg2+UniRule annotation, Mn2+UniRule annotation
  • thiamine diphosphateUniRule annotationNote: Binds 1 thiamine pyrophosphate per subunit.UniRule annotation

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. no protein annotated in this organism
  2. 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (menD)
  3. no protein annotated in this organism
  4. o-succinylbenzoate synthase (menC)
  5. no protein annotated in this organism
  6. 1,4-dihydroxy-2-naphthoyl-CoA synthase (menB), 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.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Menaquinone biosynthesis

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, Thiamine pyrophosphate

Enzyme and pathway databases

BioCyciRJOS101510:GJJ1-1995-MONOMER.
UniPathwayiUPA00079.
UPA01057; UER00164.

Names & Taxonomyi

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
Gene namesi
Name:menDUniRule annotation
Ordered Locus Names:RHA1_ro01997
OrganismiRhodococcus jostii (strain RHA1)
Taxonomic identifieri101510 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesNocardiaceaeRhodococcus
Proteomesi
  • UP000008710 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 5415412-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthasePRO_0000341814Add
BLAST

Proteomic databases

PRIDEiQ0SF82.

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi101510.RHA1_ro01997.

Structurei

3D structure databases

ProteinModelPortaliQ0SF82.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the TPP enzyme family. MenD subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C4A. Bacteria.
COG1165. LUCA.
HOGENOMiHOG000218359.
KOiK02551.
OrthoDBiEOG6NWBQW.

Family and domain databases

Gene3Di3.40.50.970. 2 hits.
HAMAPiMF_01659. MenD.
InterProiIPR004433. MenaQ_synth_MenD.
IPR029061. THDP-binding.
IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
IPR011766. TPP_enzyme-bd_C.
[Graphical view]
PfamiPF02775. TPP_enzyme_C. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]
PIRSFiPIRSF004983. MenD. 1 hit.
SUPFAMiSSF52518. SSF52518. 2 hits.
TIGRFAMsiTIGR00173. menD. 1 hit.

Sequencei

Sequence statusi: Complete.

Q0SF82-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNPSTAQATA VVDELVRGGV REVVLCPGSR NAPLAFALQA ADLEGRLRLH
60 70 80 90 100
MRIDERTAGF LALGLAVAGK RPVPIVMTSG TAVANLGPAV LEANYARVPL
110 120 130 140 150
VVLSANRPYE MLGTGANQTI EQLGLFGSQV RATISLGLAE DDAGQNSQWR
160 170 180 190 200
SAVCRVLAAA RGTRSGNAGP VHFDIPLREP LVPDVHAQGP VPQGRPGGAA
210 220 230 240 250
WTTTQHATLD VPMDLDLTPD TIVISGHGSA LRPELAGLPT VAEPTAPLHG
260 270 280 290 300
IPVHPMALPQ LKPRQAVITG RPTLHRSVSK VLADPSVAVY ALTTGPRWPD
310 320 330 340 350
VSGNVLATGT RAVVSGEPDR AWINRCRTLS EHTDKAVRAQ LAAHPKATGL
360 370 380 390 400
HVAAAVMDAL TDGDQLLLGA SNPVRDAALV SYPAPKIRVL SNRGVAGIDG
410 420 430 440 450
TVSAAVGAAL AYEEGRTVAL LGDLTFLHDA SGLLIGSGEP RPRDLTIVVA
460 470 480 490 500
NDDGGGIFEL LEQGDPQYAG VFERVFGTPH GMDLAALCAA YRVEHHLVGL
510 520 530 540
GELSTRLSAP EAPGDRGIRV LEVTTERSGL RELHAAVRAQ L
Length:541
Mass (Da):56,486
Last modified:September 5, 2006 - v1
Checksum:iE6DE20717C756BF7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000431 Genomic DNA. Translation: ABG93804.1.
RefSeqiWP_009474677.1. NC_008268.1.

Genome annotation databases

EnsemblBacteriaiABG93804; ABG93804; RHA1_ro01997.
GeneIDi4218463.
KEGGirha:RHA1_ro01997.
PATRICi23202833. VBIRhoJos26306_2018.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000431 Genomic DNA. Translation: ABG93804.1.
RefSeqiWP_009474677.1. NC_008268.1.

3D structure databases

ProteinModelPortaliQ0SF82.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi101510.RHA1_ro01997.

Proteomic databases

PRIDEiQ0SF82.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABG93804; ABG93804; RHA1_ro01997.
GeneIDi4218463.
KEGGirha:RHA1_ro01997.
PATRICi23202833. VBIRhoJos26306_2018.

Phylogenomic databases

eggNOGiENOG4105C4A. Bacteria.
COG1165. LUCA.
HOGENOMiHOG000218359.
KOiK02551.
OrthoDBiEOG6NWBQW.

Enzyme and pathway databases

UniPathwayiUPA00079.
UPA01057; UER00164.
BioCyciRJOS101510:GJJ1-1995-MONOMER.

Family and domain databases

Gene3Di3.40.50.970. 2 hits.
HAMAPiMF_01659. MenD.
InterProiIPR004433. MenaQ_synth_MenD.
IPR029061. THDP-binding.
IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
IPR011766. TPP_enzyme-bd_C.
[Graphical view]
PfamiPF02775. TPP_enzyme_C. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]
PIRSFiPIRSF004983. MenD. 1 hit.
SUPFAMiSSF52518. SSF52518. 2 hits.
TIGRFAMsiTIGR00173. menD. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: RHA1.

Entry informationi

Entry nameiMEND_RHOJR
AccessioniPrimary (citable) accession number: Q0SF82
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 2008
Last sequence update: September 5, 2006
Last modified: November 11, 2015
This is version 74 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.