RegulonDB RegulonDB 10.10: Gene Form
   

glyA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

glyA yphH hmp NsrR FNR Fur NsrR NsrR MetR MetR PurR ppGpp hmpp hmpp glyAp glyAp TSS_2845 (cluster) TSS_2845 (cluster) TSS_2844 (cluster) TSS_2844 (cluster) TSS_2843 TSS_2843 TSS_2842 TSS_2842 TSS_2841 TSS_2841 TSS_2840 TSS_2840 TSS_2839 TSS_2839 TSS_2838 TSS_2838 TSS_2837 TSS_2837 TSS_2836 (cluster) TSS_2836 (cluster)

Gene      
Name: glyA    Texpresso search in the literature
Synonym(s): ECK2548, EG10408, b2551
Genome position(nucleotides): 2684254 <-- 2685507 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.35
External database links:  
ASAP:
 ABE-0008389
CGSC:
 675
ECHOBASE:
 EB0403
ECOLIHUB:
 glyA
NCBI-GENE:
 947022
OU-MICROARRAY:
 b2551
STRING:
 511145.b2551
COLOMBOS: glyA


Shine dalgarno      
Sequence: ttagctgagtCAGGAGatgcgGAT


Product      
Name: serine hydroxymethyltransferase
Synonym(s): GlyA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol,membrane
Molecular weight: 45.317
Isoelectric point: 6.453
Motif(s):
 
Type Positions Sequence
65 -> 65 Y
85 -> 85 L
125 -> 127 GHL
216 -> 216 P
258 -> 258 P

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.1 - carbon utilization --> 1.1.3 - amino acids
  1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.1 - amino acids --> 1.5.1.10 - glycine
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.17 - formyl-THF biosynthesis
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0016020 - membrane
molecular_function GO:0003824 - catalytic activity
GO:0005515 - protein binding
GO:0016740 - transferase activity
GO:0030170 - pyridoxal phosphate binding
GO:0004372 - glycine hydroxymethyltransferase activity
GO:0008270 - zinc ion binding
GO:0042802 - identical protein binding
GO:0042803 - protein homodimerization activity
GO:0050897 - cobalt ion binding
GO:0070905 - serine binding
biological_process GO:0006545 - glycine biosynthetic process
GO:0006564 - L-serine biosynthetic process
GO:0006730 - one-carbon metabolic process
GO:0008652 - cellular amino acid biosynthetic process
GO:0046655 - folic acid metabolic process
GO:0006546 - glycine catabolic process
GO:0006565 - L-serine catabolic process
GO:0019264 - glycine biosynthetic process from serine
GO:0046653 - tetrahydrofolate metabolic process
GO:0035999 - tetrahydrofolate interconversion
Note(s): Note(s): ...[more].
Reference(s): [1] Blank D., et al., 2014
[2] Herrington MB., et al., 2013
[3] Loscha KV., et al., 2013
[4] Shen T., et al., 2013
External database links:  
DIP:
 DIP-36205N
ECOCYC:
 GLYOHMETRANS-MONOMER
ECOLIWIKI:
 b2551
INTERPRO:
 IPR015422
INTERPRO:
 IPR015424
INTERPRO:
 IPR015421
INTERPRO:
 IPR019798
INTERPRO:
 IPR039429
INTERPRO:
 IPR001085
MINT:
 P0A825
MODBASE:
 P0A825
PANTHER:
 PTHR11680
PDB:
 3G8M
PDB:
 1EQB
PDB:
 1DFO
PFAM:
 PF00464
PRIDE:
 P0A825
PRODB:
 PRO_000022816
PROSITE:
 PS00096
REFSEQ:
 NP_417046
SMR:
 P0A825
UNIPROT:
 P0A825


Operon      
Name: glyA         
Operon arrangement:
Transcription unit        Promoter
glyA


Transcriptional Regulation      
Display Regulation             
Activated by: MetR
Repressed by: PurR, MetR


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 TSS_2836 (cluster) 2684844 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_2837 2684848 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_2838 2684852 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_2839 2684858 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_2840 2684978 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_2841 2685334 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_2842 2685346 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_2843 2685533 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_2844 (cluster) 2685538 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_2845 (cluster) 2685572 reverse nd [RS-EPT-CBR] [5]


Evidence    

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


Reference(s)    

 [1] Blank D., Wolf L., Ackermann M., Silander OK., 2014, The predictability of molecular evolution during functional innovation., Proc Natl Acad Sci U S A 111(8):3044-9

 [2] Herrington MB., Sitaras C., 2013, The influence of CsgD on the expression of genes of folate metabolism and hmp in Escherichia coli K-12., Arch Microbiol 195(8):559-69

 [3] Loscha KV., Otting G., 2013, Biosynthetically directed 2H labelling for stereospecific resonance assignments of glycine methylene groups., J Biomol NMR 55(1):97-104

 [4] Shen T., Rui B., Zhou H., Zhang X., Yi Y., Wen H., Zheng H., Wu J., Shi Y., 2013, Metabolic flux ratio analysis and multi-objective optimization revealed a globally conserved and coordinated metabolic response of E. coli to paraquat-induced oxidative stress., Mol Biosyst 9(1):121-32

 [5] 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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