Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
twitter

MetaCyc Enzyme: purine nucleotidase

Gene: yrfG Accession Numbers: G7742 (MetaCyc), b3399, ECK3386

Species: Escherichia coli K-12 substr. MG1655

Summary:
YrfG is a purine nucleotidase belonging to the superfamily of haloacid dehalogenase (HAD)-like hydrolases. It shows a low level of discrimination between its preferred substrates [Kuznetsova06].

Locations: cytosol

Map Position: [3,526,691 -> 3,527,359]

Molecular Weight of Polypeptide: 25.399 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011092 , EchoBASE:EB2764 , EcoGene:EG12928 , EcoliWiki:b3399 , ModBase:P64636 , OU-Microarray:b3399 , PortEco:yrfG , Protein Model Portal:P64636 , RefSeq:NP_417858 , RegulonDB:G7742 , SMR:P64636 , String:511145.b3399 , UniProt:P64636

Relationship Links: InterPro:IN-FAMILY:IPR005833 , InterPro:IN-FAMILY:IPR006402 , InterPro:IN-FAMILY:IPR006439 , InterPro:IN-FAMILY:IPR023214 , Pfam:IN-FAMILY:PF13419 , Prints:IN-FAMILY:PR00413

Gene-Reaction Schematic: ?

Instance reactions of [a ribonucleoside 5'-monophosphate + H2O → a ribonucleoside + phosphate] (3.1.3.5):
i1: IMP + H2O → inosine + phosphate (3.1.3.5)

i2: GMP + H2O → guanosine + phosphate (3.1.3.5)

GO Terms:

Biological Process: GO:0016311 - dephosphorylation Inferred from experiment [Kuznetsova06]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment [Kuznetsova06]
GO:0008477 - purine nucleosidase activity Inferred from experiment [Kuznetsova06]
GO:0030145 - manganese ion binding Inferred from experiment [Kuznetsova06]
GO:0050483 - IMP 5'-nucleotidase activity Inferred from experiment [Kuznetsova06]
GO:0050484 - GMP 5'-nucleotidase activity Inferred from experiment [Kuznetsova06]
GO:0008253 - 5'-nucleotidase activity Inferred by computational analysis [GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

Gene Class: UNCLASSIFIED

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: inosine-5'-phosphate phosphohydrolase (purine nucleotidase)

Synonyms: HAD8

IMP + H2O <=> inosine + phosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Cofactors or Prosthetic Groups: Mg2+ [Kuznetsova06]

Kinetic Parameters:

Substrate
Km (μM)
Citations
IMP
1200.0
[Kuznetsova06]


Enzymatic reaction of: guanosine-5'-phosphate phosphohydrolase (purine nucleotidase)

Synonyms: HAD8

GMP + H2O <=> guanosine + phosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for GMP: FMN [Kuznetsova06 ]

In Pathways: purine nucleotides degradation II (aerobic) , guanosine nucleotides degradation III

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Cofactors or Prosthetic Groups: Mg2+ [Kuznetsova06]

Kinetic Parameters:

Substrate
Km (μM)
Citations
GMP
1900.0
[Kuznetsova06]


Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 9
[UniProt12]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity.
Active-Site 9
[UniProt12]
UniProt: Nucleophile; Non-Experimental Qualifier: by similarity.
Protein-Segment 9 -> 11
[UniProt12]
UniProt: Substrate; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 11
[UniProt12]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 149
[UniProt12]
UniProt: Substrate binding; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 174
[UniProt12]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity.

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Kuznetsova06: Kuznetsova E, Proudfoot M, Gonzalez CF, Brown G, Omelchenko MV, Borozan I, Carmel L, Wolf YI, Mori H, Savchenko AV, Arrowsmith CH, Koonin EV, Edwards AM, Yakunin AF (2006). "Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family." J Biol Chem 281(47):36149-61. PMID: 16990279

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

UniProt12: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Sat Dec 20, 2014, biocyc12.