nei:Gene Product(s): Difference between revisions

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===Notes===
===Notes===
Kinetic properties of Nei are described in <ref name='PMID:10862773'/>
* Kinetic properties of Nei are described in <ref name='PMID:10862773'/>
Structures of active and inactive mutants described in <ref name='PMID:16145054'/>
* Structures of active and inactive mutants described in <ref name='PMID:16145054'/>
* Catalytically important residues E2 and R252


==Gene Product Resources==
==Gene Product Resources==

Revision as of 17:45, 11 December 2009

{{#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

Nei

Synonyms

endonuclease VIII[1], 5-formyluracil/5-hydroxymethyluracil DNA glycosylase[1], B0714[2][1], Nei[2][1]

Product description

endonuclease VIII[2][3]

DNA glycosylase/apurinic lyase, deoxyinosine-specific; endonuclease VIII[4]

EC number (for enzymes)
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Notes

Function

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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(s) Evidence Code with/from Aspect Notes Status
GO:0000703

oxidized pyrimidine base lesion DNA N-glycosylase activity

GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01253

F

Seeded from EcoCyc [5]

complete

GO:0003676

nucleic acid binding

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010979

F

Seeded from EcoCyc [5]

complete

GO:0003677

DNA binding

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR015886
SP_KW:KW-0238

F

Seeded from EcoCyc 12.5 [6]

complete

GO:0003684

damaged DNA binding

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012319

F

Seeded from EcoCyc 12.5 [6]

complete

GO:0003824

catalytic activity

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR015886
SP_KW:KW-0511

F

Seeded from EcoCyc 12.5 [6]

complete

GO:0003906

DNA-(apurinic or apyrimidinic site) lyase activity

GO_REF:0000003
GO_REF:0000020

IEA: Inferred from Electronic Annotation

EC:4.2.99.18
HAMAP:MF_01253

F

Seeded from EcoCyc 12.5 [6]

complete

GO:0006281

DNA repair

GO_REF:0000002
GO_REF:0000004
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR000214
SP_KW:KW-0234
HAMAP:MF_01253

P

Seeded from EcoCyc 12.5 [6]

complete

GO:0006284

base-excision repair

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012319

P

Seeded from EcoCyc [5]

complete

GO:0006289

nucleotide-excision repair

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015886

P

Seeded from EcoCyc [5]

complete

GO:0006974

response to DNA damage stimulus

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0227

P

Seeded from EcoCyc [5]

complete

GO:0008152

metabolic process

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326

P

Seeded from EcoCyc [5]

complete

GO:0008270

zinc ion binding

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR000214
InterPro:IPR012319
InterPro:IPR015886
SP_KW:KW-0862

F

Seeded from EcoCyc 12.5 [6]

complete

GO:0008534

oxidized purine base lesion DNA N-glycosylase activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012319

F

Seeded from EcoCyc 12.5 [6]

complete

GO:0016787

hydrolase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc [5]

complete

GO:0016798

hydrolase activity, acting on glycosyl bonds

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326

F

Seeded from EcoCyc [5]

complete

GO:0016829

lyase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0456

F

Seeded from EcoCyc [5]

complete

GO:0046872

metal ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc [5]

complete

GO:0005737

cytoplasm

C

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0016799

hydrolase activity, hydrolyzing N-glycosyl compounds

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000214
InterPro:IPR012319
InterPro:IPR015886
InterPro:IPR015887

F

Seeded from EcoCyc [5]

complete

GO:0003906

DNA-(apurinic or apyrimidinic site) lyase activity

PMID:10862773[7]

IDA: Inferred from Direct Assay

F

complete

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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

hupB

PMID:15690043[8]

Experiment(s):EBI-882379

Protein

lpdA

PMID:15690043[8]

Experiment(s):EBI-882379

Protein

groL

PMID:15690043[8]

Experiment(s):EBI-882379

Protein

rplD

PMID:15690043[8]

Experiment(s):EBI-882379

Protein

rplU

PMID:15690043[8]

Experiment(s):EBI-882379

Protein

rpmB

PMID:15690043[8]

Experiment(s):EBI-882379

Protein

rpsD

PMID:15690043[8]

Experiment(s):EBI-882379

Protein

rpsN

PMID:15690043[8]

Experiment(s):EBI-882379

Protein

slyD

PMID:15690043[8]

Experiment(s):EBI-882379

Protein

nadE

PMID:16606699[9]

Experiment(s):EBI-1137778

Protein

prs

PMID:16606699[9]

Experiment(s):EBI-1137778

Protein

groL

PMID:16606699[9]

Experiment(s):EBI-1137778

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Notes

Localization

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

Compartment Description Evidence Source Notes
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Notes

Structure and Physical Properties

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

Sequence

at EcoCyc 

MPEGPEIRRA ADNLEAAIKG KPLTDVWFAF PQLKPYQSQL IGQHVTHVET RGKALLTHFS
NDLTLYSHNQ LYGVWRVVDT GEEPQTTRVL RVKLQTADKT ILLYSASDIE MLTPEQLTTH
PFLQRVGPDV LDPNLTPEVV KERLLSPRFR NRQFAGLLLD QAFLAGLGNY LRVEILWQVG
LTGNHKAKDL NAAQLDALAH ALLEIPRFSY ATRGQVDENK HHGALFRFKV FHRDGEPCER
CGSIIEKTTL SSRPFYWCPG CQH
Length

263

Mol. Wt

29.845 kDa

pI

8.0 (calculated)

Extinction coefficient

32,430 - 32,930 (calc based on 7 Y, 4 W, and 4 C residues)

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Domains/Motifs/Modification Sites

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

Type Residues Description Notes

Initiator Methionine

1

Removed

UniProt:P50465

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<motif_map/>

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

Structures

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

Models

View models at:

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Structure figures

Notes

  • Kinetic properties of Nei are described in [7]
  • Structures of active and inactive mutants described in [10]
  • Catalytically important residues E2 and R252

Gene Product Resources

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

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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

Database Accession Notes

EcoCyc (EcoliWiki Page)

EcoCyc:G6383-MONOMER

UniProt (EcoliWiki Page)

UniProt:P50465

PFAM (EcoliWiki Page)

PFAM:PF01149

RefSeq (EcoliWiki Page)

RefSeq:NP_415242


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Notes

Links

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Name URL Comments
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References

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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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 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. ↑ 5.00 5.01 5.02 5.03 5.04 5.05 5.06 5.07 5.08 5.09 5.10 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  6. ↑ 6.0 6.1 6.2 6.3 6.4 6.5 6.6 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  7. ↑ 7.0 7.1 Hazra, TK et al. (2000) Characterization of a novel 8-oxoguanine-DNA glycosylase activity in Escherichia coli and identification of the enzyme as endonuclease VIII. J. Biol. Chem. 275 27762-7 PubMed
  8. ↑ 8.0 8.1 8.2 8.3 8.4 8.5 8.6 8.7 8.8 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  9. ↑ 9.0 9.1 9.2 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  10. ↑ Golan, G et al. (2005) Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility. Nucleic Acids Res. 33 5006-16 PubMed

Categories

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