RegulonDB RegulonDB 10.9: Gene Form
   

menD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

menD menF menB menH terminator TSS_2521 TSS_2521 TSS_2520 TSS_2520 TSS_2519 (cluster) TSS_2519 (cluster) menBp menBp

Gene      
Name: menD    Texpresso search in the literature
Synonym(s): ECK2258, EG10579, b2264
Genome position(nucleotides): 2377589 <-- 2379259 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
58.11
External database links:  
ASAP:
ABE-0007482
CGSC:
517
ECHOBASE:
EB0574
ECOLIHUB:
menD
OU-MICROARRAY:
b2264
STRING:
511145.b2264
COLOMBOS: menD


Product      
Name: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Synonym(s): MenD
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 61.367
Isoelectric point: 6.547
Motif(s):
 
Type Positions Sequence
163 -> 183 GVHINCPFAEPLYGEMDDTGL
415 -> 535 ASGIDGLLSTAAGVQRASGKPTLAIVGDLSALYDLNALALLRQVSAPLVLIVVNNNGGQIFSLLPTPQSERERFYLMPQNVHFEHAAAMFELKYHRPQNWQELETAFADAWRTPTTTVIEM
42 -> 42 A
398 -> 398 D
11 -> 140 AAVILEALTRHGVRHICIAPGSRSTPLTLAAAENSAFIHHTHFDERGLGHLALGLAKVSKQPVAVIVTSGTAVANLYPALIEAGLTGEKLILLTADRPPELIDCGANQAIRQPGMFASHPTHSISLPRPT

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.7 - anaerobic respiration
  1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.3 - cofactors, small molecule carriers --> 1.5.3.11 - menaquinone, ubiquinone
Gene Ontology Terms (GO)  
molecular_function GO:0003824 - catalytic activity
GO:0016740 - transferase activity
GO:0046872 - metal ion binding
GO:0019142 - 2-hydroxyglutarate synthase activity
GO:0000287 - magnesium ion binding
GO:0030145 - manganese ion binding
GO:0030976 - thiamine pyrophosphate binding
GO:0042803 - protein homodimerization activity
GO:0070204 - 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity
biological_process GO:0009234 - menaquinone biosynthetic process
External database links:  
DIP:
DIP-10185N
ECOCYC:
MEND-MONOMER
ECOLIWIKI:
b2264
INTERPRO:
IPR032264
INTERPRO:
IPR029061
INTERPRO:
IPR004433
INTERPRO:
IPR011766
INTERPRO:
IPR012001
MODBASE:
P17109
PANTHER:
PTHR42916
PDB:
3FLM
PDB:
5Z2U
PDB:
5Z2R
PDB:
5Z2P
PDB:
2JLA
PDB:
2JLC
PDB:
3HWW
PDB:
3HWX
PDB:
5EJ4
PDB:
5EJ5
PDB:
5EJ6
PDB:
5EJ7
PDB:
5EJ8
PDB:
5EJ9
PDB:
5EJA
PDB:
5EJM
PFAM:
PF02776
PFAM:
PF02775
PFAM:
PF16582
PRIDE:
P17109
PRODB:
PRO_000023203
REFSEQ:
NP_416767
SMR:
P17109
UNIPROT:
P17109


Operon      
Name: menFDHBCE         
Operon arrangement:
Transcription unit        Promoter
menD-yfbB-menBCE
menBCE
menFD-yfbB-menBCE


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter menBp 2376887 reverse nd [AIPP], [ICWHO] [1], [2]
  promoter TSS_2519 (cluster) 2376914 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [3]
  promoter TSS_2520 2379245 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_2521 2379281 reverse nd [RS-EPT-CBR] [3]


Evidence    

 [AIPP] Automated inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [2] Sharma V., Suvarna K., Meganathan R., Hudspeth ME., 1992, Menaquinone (vitamin K2) biosynthesis: nucleotide sequence and expression of the menB gene from Escherichia coli., J Bacteriol 174(15):5057-62

 [3] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.


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