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Protein

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

Gene

menD

Organism
Staphylococcus haemolyticus (strain JCSC1435)
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: 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.

Pathway: 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

BioCyciSHAE279808:GJX7-1974-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:SH1919
OrganismiStaphylococcus haemolyticus (strain JCSC1435)
Taxonomic identifieri279808 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesStaphylococcus
ProteomesiUP000000543 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 5565562-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthasePRO_0000341865Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi279808.SH1919.

Structurei

3D structure databases

ProteinModelPortaliQ4L547.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1165.
HOGENOMiHOG000218359.
KOiK02551.
OMAiQKPWLLE.
OrthoDBiEOG6NWBQW.

Family and domain databases

Gene3Di3.40.50.970. 2 hits.
HAMAPiMF_01659. MenD.
InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
IPR004433. 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.
SUPFAMiSSF52467. SSF52467. 1 hit.
SSF52518. SSF52518. 2 hits.
TIGRFAMsiTIGR00173. menD. 1 hit.

Sequencei

Sequence statusi: Complete.

Q4L547-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNHNEALTKQ VYTFASELYA YGVREVVISP GSRSTPLAIA FEAHPNIKTW
60 70 80 90 100
IHPDERSAAF FALGLIKGSE RPVAILCTSG TAAANYTPAI AESQISRIPL
110 120 130 140 150
IVLTSDRPHE LRSVGAPQAI NQVNMFANYV NFQFDMPVAD GTDYMLDAIY
160 170 180 190 200
YQMQIASQYL YGPHRGPIHF NLPFREPLTP NLERQEWLTS YSKKLPHYQK
210 220 230 240 250
NINVQDIRHI LKEKKGLIIV GDMQHQAIDQ ILTYATVHDI PILADPLSQL
260 270 280 290 300
RKYNHPNVIT TYDLYYRAGL DIDVDFVIRV GKPVISKKLN QWLKRTNAYQ
310 320 330 340 350
ILVQNNDKID VFPTPPSISY EISANDFFRN LIEEAAVDRK DWINMWRTLE
360 370 380 390 400
SQARNTIDKH MTNATDEAAF VKILIDKLTK DDAIFVSNSM PVRDIDNLLY
410 420 430 440 450
NSEVEVYANR GANGIDGVVS TAIGMAVHKK ITLIIGDLAF YHDMNGLLMA
460 470 480 490 500
KINNINLNIV LLNNDGGGIF SYLPQKASAE AYFERLFGTP TGLNFEYTAL
510 520 530 540 550
LYDFTFKRFN TVADFTQEKL SHVNSHIYEM VTNRDDNMSQ HQILYKKLSG

ILNVTL
Length:556
Mass (Da):63,095
Last modified:August 2, 2005 - v1
Checksum:iFE88BE461C5A72D0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006716 Genomic DNA. Translation: BAE05228.1.
RefSeqiWP_011276189.1. NC_007168.1.
YP_253834.1. NC_007168.1.

Genome annotation databases

EnsemblBacteriaiBAE05228; BAE05228; SH1919.
KEGGisha:SH1919.
PATRICi19619943. VBIStaHae67511_1894.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006716 Genomic DNA. Translation: BAE05228.1.
RefSeqiWP_011276189.1. NC_007168.1.
YP_253834.1. NC_007168.1.

3D structure databases

ProteinModelPortaliQ4L547.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi279808.SH1919.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAE05228; BAE05228; SH1919.
KEGGisha:SH1919.
PATRICi19619943. VBIStaHae67511_1894.

Phylogenomic databases

eggNOGiCOG1165.
HOGENOMiHOG000218359.
KOiK02551.
OMAiQKPWLLE.
OrthoDBiEOG6NWBQW.

Enzyme and pathway databases

UniPathwayiUPA00079.
UPA01057; UER00164.
BioCyciSHAE279808:GJX7-1974-MONOMER.

Family and domain databases

Gene3Di3.40.50.970. 2 hits.
HAMAPiMF_01659. MenD.
InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
IPR004433. 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.
SUPFAMiSSF52467. SSF52467. 1 hit.
SSF52518. SSF52518. 2 hits.
TIGRFAMsiTIGR00173. menD. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Whole-genome sequencing of Staphylococcus haemolyticus uncovers the extreme plasticity of its genome and the evolution of human-colonizing staphylococcal species."
    Takeuchi F., Watanabe S., Baba T., Yuzawa H., Ito T., Morimoto Y., Kuroda M., Cui L., Takahashi M., Ankai A., Baba S., Fukui S., Lee J.C., Hiramatsu K.
    J. Bacteriol. 187:7292-7308(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: JCSC1435.

Entry informationi

Entry nameiMEND_STAHJ
AccessioniPrimary (citable) accession number: Q4L547
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 2008
Last sequence update: August 2, 2005
Last modified: June 24, 2015
This is version 75 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.