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Escherichia coli K-12 substr. MG1655 Enzyme: 2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase



Gene: cpdB Accession Numbers: EG10160 (EcoCyc), b4213, ECK4209

Regulation Summary Diagram: ?

Summary:
cpdB from E. coli K-12 encodes a 2',3'-cyclic nucleotide 2'-phosphodiesterase [Liu86]. The enzyme has been purified from E. coli B and characterised as a bifunctional enzyme which catalyzes two sequential reactions: the first enzymatic activity is a 2',3'-cyclic nucleotide 2'-phosphodiesterase in which a 2',3'-cyclic nucleotide is converted to a 3'-nucleotide; the second activity is a 3'-nucleotidase which yields a ribonucleotide and phosphate [Anraku64, Anraku64a]. Kinetic analyses suggest that the enzyme has two distinct active sites [Anraku64a]. The physiological role of CpdB may be to break down ribonucleotide 2',3'-cyclic phosphates which are formed when RNA is digested by ribosome bound RNase [Anraku64a].

cpdB expression is modulated by carbon source availability - an increase in enzyme activity is observed when E. coli is grown with limiting glucose, glycerol or succinate as the sole carbon source - and a putative CRP binding site is located in the promoter region of the cpdB gene [Liu90].

Gene Citations: [Beacham80]

Locations: periplasmic space

Map Position: [4,432,645 <- 4,434,588] (95.54 centisomes)
Length: 1944 bp / 647 aa

Molecular Weight of Polypeptide: 70.832 kD (from nucleotide sequence), 67.0 kD (experimental) [Liu86 ]

pI: 5.77

Unification Links: ASAP:ABE-0013782 , CGSC:909 , DIP:DIP-9311N , EchoBASE:EB0158 , EcoGene:EG10160 , EcoliWiki:b4213 , Mint:MINT-1228170 , ModBase:P08331 , OU-Microarray:b4213 , PortEco:cpdB , PR:PRO_000022322 , Pride:P08331 , Protein Model Portal:P08331 , RefSeq:NP_418634 , RegulonDB:EG10160 , SMR:P08331 , String:511145.b4213 , UniProt:P08331

Relationship Links: InterPro:IN-FAMILY:IPR004843 , InterPro:IN-FAMILY:IPR006146 , InterPro:IN-FAMILY:IPR006179 , InterPro:IN-FAMILY:IPR006294 , InterPro:IN-FAMILY:IPR008334 , Panther:IN-FAMILY:PTHR11575 , Pfam:IN-FAMILY:PF00149 , Pfam:IN-FAMILY:PF02872 , Prints:IN-FAMILY:PR01607 , Prosite:IN-FAMILY:PS00785 , Prosite:IN-FAMILY:PS00786

In Paralogous Gene Group: 137 (2 members)

Gene-Reaction Schematic: ?

Instance reactions of [a nucleoside 3'-phosphate + H2O → a ribonucleoside + phosphate] (3.1.3.6):
i1: cytidine-3'-monophosphate + H2O → cytidine + phosphate (3.1.3.6)

i2: uridine 3'-monophosphate[periplasmic space] + H2O[periplasmic space] → uridine[periplasmic space] + phosphate[periplasmic space] (3.1.3.6)

i3: adenosine 3'-monophosphate + H2O → adenosine + phosphate (3.1.3.6)

i4: guanosine 3'-monophosphate[periplasmic space] + H2O[periplasmic space] → guanosine[periplasmic space] + phosphate[periplasmic space] (3.1.3.6)

Instance reactions of [a 2',3'-cyclic nucleoside phosphate[periplasmic space] + H2O[periplasmic space] → a nucleoside 3'-phosphate[periplasmic space] + H+[periplasmic space]] (3.1.4.16):
i5: uridine 2'3'-cyclic monophosphate[periplasmic space] + H2O[periplasmic space] → uridine 3'-monophosphate[periplasmic space] + H+[periplasmic space] (3.1.4.16)

i6: adenosine 2',3'-cyclic monophosphate[periplasmic space] + H2O[periplasmic space] → adenosine 3'-monophosphate[periplasmic space] + H+[periplasmic space] (3.1.4.16)

i7: guanosine 2',3'-cyclic monophosphate[periplasmic space] + H2O[periplasmic space] → guanosine 3'-monophosphate[periplasmic space] + H+[periplasmic space] (3.1.4.16)

i8: cytidine 2',3'-cyclic monophosphate[periplasmic space] + H2O[periplasmic space] → cytidine-3'-monophosphate[periplasmic space] + H+[periplasmic space] (3.1.4.16)

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0009166 - nucleotide catabolic process Inferred from experiment Inferred by computational analysis [GOA01, Liu90]
GO:0016311 - dephosphorylation Inferred from experiment Inferred by computational analysis [Liu86, Anraku64a, GOA01a]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0009117 - nucleotide metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0008254 - 3'-nucleotidase activity Inferred from experiment Inferred by computational analysis [GOA01a, Anraku64a, Liu86]
GO:0008663 - 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Anraku64a, Liu86]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003824 - catalytic activity Inferred by computational analysis [UniProtGOA11]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016788 - hydrolase activity, acting on ester bonds Inferred by computational analysis [GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space Inferred from experiment Inferred by computational analysis [DiazMejia09, Han13, LopezCampistrou05, Brockman68]
GO:0042597 - periplasmic space Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, Brockman68]

MultiFun Terms: metabolism central intermediary metabolism nucleotide and nucleoside conversions

Essentiality data for cpdB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Last-Curated ? 04-Jul-2011 by Mackie A , Macquarie University


Enzymatic reaction of: 3'-nucleotidase (2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase)

Synonyms: 3'-ribonucleotide phosphohydrolase

EC Number: 3.1.3.6

a nucleoside 3'-phosphate[periplasmic space] + H2O[periplasmic space] <=> a ribonucleoside[periplasmic space] + phosphate[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

Alternative Substrates [Comment 5]:

Activators (Unknown Mechanism): Co2+ [Anraku64]

Inhibitors (Unknown Mechanism): Cu2+ [Anraku64] , Zn2+ [Anraku64] , EDTA [Anraku64] , potassium cyanide [Anraku64] , a ribonucleic acid [Anraku64a]


Enzymatic reaction of: 2',3'-cyclic nucleotide 2'-phosphodiesterase (2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase)

Synonyms: nucleoside-2',3'-cyclic-phosphate 3'-nucleotidohydrolase, 2',3'-cyclic phosphodiesterase

EC Number: 3.1.4.16

a 2',3'-cyclic nucleoside phosphate[periplasmic space] + H2O[periplasmic space] <=> a nucleoside 3'-phosphate[periplasmic space] + H+[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

Alternative Substrates [Comment 6]:

Activators (Unknown Mechanism): Co2+ [Anraku64]

Inhibitors (Unknown Mechanism): Cu2+ [Anraku64] , Zn2+ [Anraku64] , EDTA [Anraku64] , potassium cyanide [Anraku64]


Enzymatic reaction of: uridine 3' nucleotidase (2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase)

EC Number: 3.1.3.6

uridine 3'-monophosphate[periplasmic space] + H2O[periplasmic space] <=> uridine[periplasmic space] + phosphate[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.


Enzymatic reaction of: adenosine 3' nucleotidase (2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase)

EC Number: 3.1.3.6

adenosine 3'-monophosphate[periplasmic space] + H2O[periplasmic space] <=> adenosine[periplasmic space] + phosphate[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.


Enzymatic reaction of: guanosine 3' nucleotidase (2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase)

EC Number: 3.1.3.6

guanosine 3'-monophosphate[periplasmic space] + H2O[periplasmic space] <=> guanosine[periplasmic space] + phosphate[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.


Enzymatic reaction of: cytidine 3' nucleotidase (2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase)

EC Number: 3.1.3.6

cytidine-3'-monophosphate[periplasmic space] + H2O[periplasmic space] <=> cytidine[periplasmic space] + phosphate[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.


Enzymatic reaction of: adenosine 2'3'-cyclic phosphodiesterase (2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase)

EC Number: 3.1.4.16

adenosine 2',3'-cyclic monophosphate[periplasmic space] + H2O[periplasmic space] <=> adenosine 3'-monophosphate[periplasmic space] + H+[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

Kinetic Parameters:

Substrate
Km (μM)
Citations
adenosine 2',3'-cyclic monophosphate
5300.0
[Anraku64a]


Enzymatic reaction of: cytidine 2'3'-cyclic phosphodiesterase (2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase)

EC Number: 3.1.4.16

cytidine 2',3'-cyclic monophosphate[periplasmic space] + H2O[periplasmic space] <=> cytidine-3'-monophosphate[periplasmic space] + H+[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

Kinetic Parameters:

Substrate
Km (μM)
Citations
cytidine 2',3'-cyclic monophosphate
3200.0
[Anraku64a]


Enzymatic reaction of: uridine 2'3'-cyclic phosphodiesterase (2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase)

EC Number: 3.1.4.16

uridine 2'3'-cyclic monophosphate[periplasmic space] + H2O[periplasmic space] <=> uridine 3'-monophosphate[periplasmic space] + H+[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

Kinetic Parameters:

Substrate
Km (μM)
Citations
uridine 2'3'-cyclic monophosphate
5300.0
[Anraku64a]


Enzymatic reaction of: guanosine 2'3'-cyclic phosphodiesterase (2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase)

EC Number: 3.1.4.16

guanosine 2',3'-cyclic monophosphate[periplasmic space] + H2O[periplasmic space] <=> guanosine 3'-monophosphate[periplasmic space] + H+[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

Kinetic Parameters:

Substrate
Km (μM)
Citations
guanosine 2',3'-cyclic monophosphate
3000.0
[Anraku64a]


Sequence Features

Feature Class Location Citations Comment
Signal-Sequence 1 -> 19
[Link97, UniProt11]
.
Chain 20 -> 647
[UniProt09]
UniProt: 2',3'-cyclic-nucleotide 2'- phosphodiesterase;
Metal-Binding-Site 31
[UniProt10]
UniProt: Divalent metal cation 1; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 33
[UniProt10]
UniProt: Divalent metal cation 1; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 76
[UniProt10]
UniProt: Divalent metal cation 1; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 116
[UniProt10]
UniProt: Divalent metal cation 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 225
[UniProt10]
UniProt: Divalent metal cation 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 257
[UniProt10]
UniProt: Divalent metal cation 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 259
[UniProt10]
UniProt: Divalent metal cation 1; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 316
[Liu86, UniProt10a]
Alternate sequence: A → G; UniProt: (in Ref. 1; AAA23597);
Amino-Acid-Sites-That-Bind 440
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 528 -> 552
[Liu86, UniProt10a]
Alternate sequence: GKPIDPNAMFLVATNNYRAYGGKFA → ASRLIRTPCSWLPPITIALTGQIC; UniProt: (in Ref. 1; AAA23597);
Protein-Segment 544 -> 550
[UniProt10]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b4213 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10160; confirmed by SwissProt match.


References

Anraku64: Anraku Y (1964). "A new cyclic phosphodiesterase having a 3'-nucleotidase activity from Escherichia coli B. I. Purification and some properties of the enzyme." J Biol Chem 1964;239(10):3412-3419. PMID: 14245396

Anraku64a: Anraku Y (1964). "A new cyclic phosphodiesterase having a 3'-nucleotidase activity from Escherichia coli B. II. Further studies on substrate specificity and mode of action of the enzyme." J Biol Chem 239;3420-4. PMID: 14245397

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Beacham80: Beacham IR, Garrett S (1980). "Isolation of Escherichia coli mutants (cpdB) deficient in periplasmic 2':3'-cyclic phosphodiesterase and genetic mapping of the cpdB locus." J Gen Microbiol 119(1);31-4. PMID: 6251162

Brockman68: Brockman RW, Heppel LA (1968). "On the localization of alkaline phosphatase and cyclic phosphodiesterase in Escherichia coli." Biochemistry 7(7);2554-62. PMID: 4298222

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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Han13: Han MJ, Kim JY, Kim JA (2013). "Comparison of the large-scale periplasmic proteomes of the Escherichia coli K-12 and B strains." J Biosci Bioeng. PMID: 24140104

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

Liu86: Liu J, Burns DM, Beacham IR (1986). "Isolation and sequence analysis of the gene (cpdB) encoding periplasmic 2',3'-cyclic phosphodiesterase." J Bacteriol 1986;165(3);1002-10. PMID: 3005231

Liu90: Liu J, Beacham IR (1990). "Transcription and regulation of the cpdB gene in Escherichia coli K12 and Salmonella typhimurium LT2: evidence for modulation of constitutive promoters by cyclic AMP-CRP complex." Mol Gen Genet 1990;222(1);161-5. PMID: 2172762

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Fri Dec 19, 2014, biocyc13.