cdd:Gene Product(s)

From EcoliWiki
Jump to: navigation, search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

Cdd

Synonyms

cytidine/deoxycytidine deaminase[1], B2143[2][1], Cdd[2][1] , ECK2136, JW2131, b2143

Product description

Cdd[2][3];

Component of CYTIDEAM-CPLX[2]

Cytidine deaminase; 2-deoxycytidine deaminase; mutants are 5-fluorodeoxycytidine resistant; binds Zn(II)[4]

EC number (for enzymes)
edit table

<protect></protect>

Notes

Function

[back to top]


<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0001884

pyrimidine nucleoside binding

PMID:3910086[5]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016193

F

Seeded from EcoCyc (v14.0)

complete

GO:0004126

cytidine deaminase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01558

F

Seeded from EcoCyc (v14.0)

complete

GO:0004126

cytidine deaminase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006263

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

PMID:8289286[6]

IDA: Inferred from Direct Assay

F

complete

GO:0004126

cytidine deaminase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013171

F

Seeded from EcoCyc (v14.0)

complete

GO:0001884

pyrimidine nucleoside binding

PMID:3910086[5]

IDA: Inferred from Direct Assay

F

cytidine binding

complete

GO:0004126

cytidine deaminase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020797

F

Seeded from EcoCyc (v14.0)

complete

GO:0004126

cytidine deaminase activity

PMID:4944311[7]

IDA: Inferred from Direct Assay

F

complete

GO:0004126

cytidine deaminase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.5.4.5

F

Seeded from EcoCyc (v14.0)

complete

GO:0015949

nucleobase, nucleoside and nucleotide interconversion

PMID:4944311[7]

IDA: Inferred from Direct Assay

P

complete

GO:0005829

cytosol

PMID:16858726[8]

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0015949

nucleobase, nucleoside and nucleotide interconversion

PMID:4944312[9]

IDA: Inferred from Direct Assay

P

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002125

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006263

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013171

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016192

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020797

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0862

F

Seeded from EcoCyc (v14.0)

complete

GO:0046087

cytidine metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006263

P

Seeded from EcoCyc (v14.0)

complete

GO:0046087

cytidine metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020797

P

Seeded from EcoCyc (v14.0)

complete

edit table

Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

Subunits of CYTIDEAM-CPLX

could be indirect

RNA

cytidine

substrate

PMID:4944311[7]

kinetic assay

RNA

N4-methylcytidine

substrate

PMID:4944311[7]

kinetic assay

RNA

3,4,5,6-tetrahydrouridine

inhibitor

PMID:4944311[7]

kinetic assay

RNA

5,6-dihydrouridine

inhibitor

PMID:4944311[7]

kinetic assay

edit table

</protect>

Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
edit table

<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MHPRFQTAFA QLADNLQSAL EPILADKYFP ALLTGEQVSS LKSATGLDED ALAFALLPLA
AACARTPLSN FNVGAIARGV SGTWYFGANM EFIGATMQQT VHAEQSAISH AWLSGEKALA
AITVNYTPCG HCRQFMNELN SGLDLRIHLP GREAHALRDY LPDAFGPKDL EIKTLLMDEQ
DHGYALTGDA LSQAAIAAAN RSHMPYSKSP SGVALECKDG RIFSGSYAEN AAFNPTLPPL
QGALILLNLK GYDYPDIQRA VLAEKADAPL IQWDATSATL KALGCHSIDR VLLA
Length

294

Mol. Wt

31.54 kDa

pI

5.6 (calculated)

Extinction coefficient

29,910 - 30,535 (calc based on 9 Y, 3 W, and 5 C residues)

edit table


Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

47..143

PF00383 Cytidine and deoxycytidylate deaminase zinc-binding region

PMID:19920124[10]

Domain

157..279

PF08211 Cytidine and deoxycytidylate deaminase zinc-binding region

PMID:19920124[10]

edit table

<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=cdd taxon=562,83333 </beststructure>

Models

View models at:

edit table
</protect>

Structure figures

<protect>

</protect>

Notes

  • Physical properties and substrate/inhibitor binding/kinetic information may be found in [5] and [7]
  • Crystal structure information may be found in [6]

Gene Product Resources

[back to top]


See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16130081

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946663

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007086

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0ABF6

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10137

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10137

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946663

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000133

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0135

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]




References

[back to top]


See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 Vita, A et al. (1985) Cytidine deaminase from Escherichia coli B. Purification and enzymatic and molecular properties. Biochemistry 24 6020-4 PubMed
  6. ↑ 6.0 6.1 Betts, L et al. (1994) Cytidine deaminase. The 2.3 A crystal structure of an enzyme: transition-state analog complex. J. Mol. Biol. 235 635-56 PubMed
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 Cohen, RM & Wolfenden, R (1971) Cytidine deaminase from Escherichia coli. Purification, properties and inhibition by the potential transition state analog 3,4,5,6-tetrahydrouridine. J. Biol. Chem. 246 7561-5 PubMed
  8. ↑ Lasserre, JP et al. (2006) A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis. Electrophoresis 27 3306-21 PubMed
  9. ↑ Cohen, RM & Wolfenden, R (1971) The equilibrium of hydrolytic deamination of cytidine and N 4 -methylcytidine. J. Biol. Chem. 246 7566-8 PubMed
  10. ↑ 10.0 10.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=cdd:Gene_Product(s)&oldid=1494038"