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Protein

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

Gene

menD

Organism
Geobacillus thermodenitrificans (strain NG80-2)
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. 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.

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

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:GTNG_2773
OrganismiGeobacillus thermodenitrificans (strain NG80-2)
Taxonomic identifieri420246 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus
Proteomesi
  • UP000001578 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003417501 – 5862-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthaseAdd BLAST586

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi420246.GTNG_2773.

Structurei

3D structure databases

ProteinModelPortaliA4IS14.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C4A. Bacteria.
COG1165. LUCA.
HOGENOMiHOG000218359.
KOiK02551.
OMAiIFRILPG.
OrthoDBiPOG091H058U.

Family and domain databases

Gene3Di3.40.50.1220. 1 hit.
3.40.50.970. 2 hits.
HAMAPiMF_01659. MenD. 1 hit.
InterProiIPR029035. 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.
[Graphical view]
PfamiPF02775. TPP_enzyme_C. 1 hit.
PF16582. TPP_enzyme_M_2. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]
PIRSFiPIRSF004983. MenD. 1 hit.
SUPFAMiSSF52467. SSF52467. 1 hit.
SSF52518. SSF52518. 2 hits.
TIGRFAMsiTIGR00173. menD. 1 hit.

Sequencei

Sequence statusi: Complete.

A4IS14-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTNALSWYVA AFVDGLVQAG VTEAVISPGS RSTPLAMAMA AHSGLHFSMH
60 70 80 90 100
IDERSAAFFA LGMVKAKQRP VALVCTSGTA AANYLPAIVE AYYSRVPLVV
110 120 130 140 150
LTADRPHELR DVGAPQAIDQ LHLYGRYAKW FVDLALPEET DPMLSYARTM
160 170 180 190 200
AARAAAIAAG APAGPVHVNV PLREPLVPTI DEAVWEKVRT VAETPQIMSG
210 220 230 240 250
RATLPAENVA ALYEQLAAAK RGLIVCGALD QPGFAEAVTE LARTLDFPIL
260 270 280 290 300
ADPLSQLRAG AHDKTYVIDS YDAILKDEAV ASRLVPDVVL RFGAMPVSKP
310 320 330 340 350
LFLWLKQHRS IRQIVVDDGG WRDPTLEAAC FVRSDETVLC RQLLDIARPK
360 370 380 390 400
QKESAWSTTW REMNDIARTV LRQHLPADEW FEGKVFTELA ELLPAGATLF
410 420 430 440 450
VGNSMPIRDA DTFLFATDKP LRVLANRGAN GIDGVVSSAL GASLAASPLV
460 470 480 490 500
LVIGDLSFYH DLNGLLAAKM HGLQATIVLM NNNGGGIFSF LPQARHEGPF
510 520 530 540 550
ETLFGTPTDL TFAHAVEMYG GRYAVPHTWG EFRHHVAESL NTGGLSVIEV
560 570 580
RTSRTENVQM HRFLWERVSQ EIAKFLEQKG TEEPWN
Length:586
Mass (Da):63,933
Last modified:May 1, 2007 - v1
Checksum:i19B6D19AB40CFEC4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000557 Genomic DNA. Translation: ABO68118.1.
RefSeqiWP_011888023.1. NC_009328.1.

Genome annotation databases

EnsemblBacteriaiABO68118; ABO68118; GTNG_2773.
KEGGigtn:GTNG_2773.
PATRICi21982119. VBIGeoThe136879_2921.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000557 Genomic DNA. Translation: ABO68118.1.
RefSeqiWP_011888023.1. NC_009328.1.

3D structure databases

ProteinModelPortaliA4IS14.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi420246.GTNG_2773.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABO68118; ABO68118; GTNG_2773.
KEGGigtn:GTNG_2773.
PATRICi21982119. VBIGeoThe136879_2921.

Phylogenomic databases

eggNOGiENOG4105C4A. Bacteria.
COG1165. LUCA.
HOGENOMiHOG000218359.
KOiK02551.
OMAiIFRILPG.
OrthoDBiPOG091H058U.

Enzyme and pathway databases

UniPathwayiUPA00079.
UPA01057; UER00164.

Family and domain databases

Gene3Di3.40.50.1220. 1 hit.
3.40.50.970. 2 hits.
HAMAPiMF_01659. MenD. 1 hit.
InterProiIPR029035. 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.
[Graphical view]
PfamiPF02775. TPP_enzyme_C. 1 hit.
PF16582. TPP_enzyme_M_2. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]
PIRSFiPIRSF004983. MenD. 1 hit.
SUPFAMiSSF52467. SSF52467. 1 hit.
SSF52518. SSF52518. 2 hits.
TIGRFAMsiTIGR00173. menD. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiMEND_GEOTN
AccessioniPrimary (citable) accession number: A4IS14
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 2008
Last sequence update: May 1, 2007
Last modified: November 2, 2016
This is version 69 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

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.