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Protein

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

Gene

menD

Organism
Synechococcus sp. (strain WH7803)
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. no protein annotated in this organism
  5. no protein annotated in this organism
  6. 1,4-dihydroxy-2-naphthoyl-CoA synthase (menB)
  7. 1,4-dihydroxy-2-naphthoyl-CoA hydrolase (SynWH7803_2315)
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: phylloquinone biosynthesis

This protein is involved in the pathway phylloquinone biosynthesis, which is part of Cofactor biosynthesis.UniRule annotation
View all proteins of this organism that are known to be involved in the pathway phylloquinone biosynthesis and in Cofactor biosynthesis.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, Thiamine pyrophosphate

Enzyme and pathway databases

UniPathwayiUPA00995.
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
Gene namesi
Name:menDUniRule annotation
Ordered Locus Names:SynWH7803_1021
OrganismiSynechococcus sp. (strain WH7803)
Taxonomic identifieri32051 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaSynechococcalesSynechococcaceaeSynechococcus
Proteomesi
  • UP000001566 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003418761 – 5782-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthaseAdd BLAST578

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi32051.SynWH7803_1021.

Structurei

3D structure databases

ProteinModelPortaliA5GKI2.
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

Gene3Di3.40.50.970. 2 hits.
HAMAPiMF_01659. MenD. 1 hit.
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.

A5GKI2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLLAHLQHQ GLRQIVLCPG SRSAPLALAA GGLARQGELT LVTAIDERSA
60 70 80 90 100
AFHALGLAQA SGRATAVITT SGTAVANLLP AAVEADRSCI PLLLLTADRP
110 120 130 140 150
TRLKDCGANQ TVNQEQFLAP VCRAFLSSPG EGLHHENDVQ LQSLASSLWE
160 170 180 190 200
RALGSAGPVH LNLPFEEPLH PSEAEQQAFW SAWQPLPAAG GEHHPAEPRS
210 220 230 240 250
TPWDGPVPDW SRPGVVVAGP WRGLEADRPA YQRALQELAL TTGWPVLLDP
260 270 280 290 300
LAAAPQDLPG VIRHWDLMLP AGLPTPERSL QVLRLGPLPA SRRLEAWLRA
310 320 330 340 350
LGPGQWLISE GDCRSLDPLG LASQCSLGLA SWWDCVSPNP LSLAPGPSSL
360 370 380 390 400
LTAWRDLEAA VAGELARQLP QAGPVSEPAL MHVLPQLLPP ALPVMLAASS
410 420 430 440 450
PVRDWQAFAA ADAGQRRCFS FRGASGIDGT LSLAVGLSRE LGPLVLLTGD
460 470 480 490 500
LALLHDSNGW LLASASAPPL LVLLIDNGGG GIFGQLPIPT APAAAFDHLF
510 520 530 540 550
AMPQAVDPLA LARAHAVPTR QLASLEDLPQ ALEWGLDQRR AVLLRVCTNR
560 570
GADAALRQML RREVEQALCV VQGSTKEG
Length:578
Mass (Da):61,125
Last modified:June 12, 2007 - v1
Checksum:i19207D3D40F0E965
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CT971583 Genomic DNA. Translation: CAK23447.1.
RefSeqiWP_011932929.1. NC_009481.1.

Genome annotation databases

EnsemblBacteriaiCAK23447; CAK23447; SynWH7803_1021.
KEGGisyx:SynWH7803_1021.
PATRICi23828176. VBISynSp43824_1052.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CT971583 Genomic DNA. Translation: CAK23447.1.
RefSeqiWP_011932929.1. NC_009481.1.

3D structure databases

ProteinModelPortaliA5GKI2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi32051.SynWH7803_1021.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAK23447; CAK23447; SynWH7803_1021.
KEGGisyx:SynWH7803_1021.
PATRICi23828176. VBISynSp43824_1052.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayiUPA00995.
UPA01057; UER00164.

Family and domain databases

Gene3Di3.40.50.970. 2 hits.
HAMAPiMF_01659. MenD. 1 hit.
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...

Entry informationi

Entry nameiMEND_SYNPW
AccessioniPrimary (citable) accession number: A5GKI2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 2008
Last sequence update: June 12, 2007
Last modified: November 2, 2016
This is version 63 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.