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Protein

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

Gene

menD

Organism
Photorhabdus luminescens subsp. laumondii (strain TT01)
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

Pathway:i1,4-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. 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. 1,4-dihydroxy-2-naphthoyl-CoA hydrolase (menI)
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.

Pathway:imenaquinone 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:plu3073
OrganismiPhotorhabdus luminescens subsp. laumondii (strain TT01)
Taxonomic identifieri243265 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaePhotorhabdus
ProteomesiUP000002514 Componenti: Chromosome

Organism-specific databases

GenoListiplu3073.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 5645642-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthasePRO_0000341796Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi243265.plu3073.

Structurei

3D structure databases

ProteinModelPortaliQ7N2K3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1165.
HOGENOMiHOG000218360.
KOiK02551.
OMAiQKPWLLE.
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.

Q7N2K3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSNSAFNRRW AELLLEALTR HGLRHVCIAP GSRSTPLTIA AAANNKLICH
60 70 80 90 100
THFDERGLGH LALGLSKASR EPVAVIVTSG TAVANLYPSL IEASLTGERM
110 120 130 140 150
VFLTADRPPE LMDCGANQAI RQNGIFASHP CQTISLPRPT VDIPASWLAS
160 170 180 190 200
VIDHSMANLQ HGAVHINCPF AEPLYGNEEP AYDEWQQQLG DWWKSKTPWL
210 220 230 240 250
SQPVAKVVAE VPDWDCWQQK KGVVLAGRMS AEEGVNVAKW AKALSWPLIG
260 270 280 290 300
NALSQTGQPL PCADLWLDNP HVQEILAQAQ LVVQFGSSLI GKCLLQWQAK
310 320 330 340 350
CQPQEFWIID PIPGRLDPAN HRGKKLTCHI ADWLLAHPAQ PCIPWAQSCT
360 370 380 390 400
LWAEELIVWS EKAVNCVRTE LAGKFGEATV AYRLRELLPE RGQLFVGNSL
410 420 430 440 450
IIRLIDTLGQ LPAGYPVYSN RGASGIDGLI STAAGVQRAT AKPTLAVIGD
460 470 480 490 500
LSALYDLNSL ALLRHPSAPM VLIVVNNNGG QIFSLLPTQE EARQRFYCMP
510 520 530 540 550
QYVNFDHAAA MFGLKYASPQ NWMELQQSIK QAWQQNETTL IELKVPDREG
560
AECLQQLLKQ VAML
Length:564
Mass (Da):62,123
Last modified:December 15, 2003 - v1
Checksum:i114D626C10D4EDAE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX571869 Genomic DNA. Translation: CAE15447.1.
RefSeqiWP_011147290.1. NC_005126.1.

Genome annotation databases

EnsemblBacteriaiCAE15447; CAE15447; plu3073.
GeneIDi24170108.
KEGGiplu:plu3073.
PATRICi20510496. VBIPhoLum48522_3487.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX571869 Genomic DNA. Translation: CAE15447.1.
RefSeqiWP_011147290.1. NC_005126.1.

3D structure databases

ProteinModelPortaliQ7N2K3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243265.plu3073.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAE15447; CAE15447; plu3073.
GeneIDi24170108.
KEGGiplu:plu3073.
PATRICi20510496. VBIPhoLum48522_3487.

Organism-specific databases

GenoListiplu3073.

Phylogenomic databases

eggNOGiCOG1165.
HOGENOMiHOG000218360.
KOiK02551.
OMAiQKPWLLE.
OrthoDBiEOG6NWBQW.

Enzyme and pathway databases

UniPathwayiUPA00079.
UPA01057; UER00164.

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: TT01.

Entry informationi

Entry nameiMEND_PHOLL
AccessioniPrimary (citable) accession number: Q7N2K3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 2008
Last sequence update: December 15, 2003
Last modified: July 22, 2015
This is version 79 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

External Data

Dasty 3

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 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.