nrdD:Gene Product(s)

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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

NrdD

Synonyms

anaerobic ribonucleoside-triphosphate reductase[1], B4238[2][1], NrdD[2][1] , ECK4233, JW4197, b4238

Product description

ribonucleoside-triphosphate reductase[2][3];

Component of ribonucleoside-triphosphate reductase[2][3]; anaerobic nucleoside-triphosphate reductase activating system[2][3]

Ribonucleoside triphosphate reductase, class III, anaerobic[4]

EC number (for enzymes)
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Notes

Function

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<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:0031250

anaerobic ribonucleoside-triphosphate reductase complex

PMID:8954104[5]

IMP: Inferred from Mutant Phenotype

C

complete

GO:0015949

nucleobase, nucleoside and nucleotide interconversion

PMID:8954104[5]

IMP: Inferred from Mutant Phenotype

P

complete

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

Contributes to

GO:0004748

ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor

PMID:8954104[5]

IMP: Inferred from Mutant Phenotype

F

replaces obsoleteGO:0016961

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

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:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012833

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

P

Seeded from EcoCyc (v14.0)

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

Subunits of ribonucleoside-triphosphate reductase

could be indirect

Protein

nadE

PMID:16606699[6]

Experiment(s):EBI-1147734

Protein

metG

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

ybiS

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

yohN

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

nrdG

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

Subunits of anaerobic nucleoside-triphosphate reductase activating system

could be indirect


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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 Reference/Source Notes
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Notes

Structure and Physical Properties

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<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 

MTPHVMKRDG CKVPFKSERI KEAILRAAKA AEVDDADYCA TVAAVVSEQM QGRNQVDINE
IQTAVENQLM SGPYKQLARA YIEYRHDRDI EREKRGRLNQ EIRGLVEQTN ASLLNENANK
DSKVIPTQRD LLAGIVAKHY ARQHLLPRDV VQAHERGDIH YHDLDYSPFF PMFNCMLIDL
KGMLTQGFKM GNAEIEPPKS ISTATAVTAQ IIAQVASHIY GGTTINRIDE VLAPFVTASY
NKHRKTAEEW NIPDAEGYAN SRTIKECYDA FQSLEYEVNT LHTANGQTPF VTFGFGLGTS
WESRLIQESI LRNRIAGLGK NRKTAVFPKL VFAIRDGLNH KKGDPNYDIK QLALECASKR
MYPDILNYDQ VVKVTGSFKT PMGCRSFLGV WENENGEQIH DGRNNLGVIS LNLPRIALEA
KGDEATFWKL LDERLVLARK ALMTRIARLE GVKARVAPIL YMEGACGVRL NADDDVSEIF
KNGRASISLG YIGIHETINA LFGGEHVYDN EQLRAKGIAI VERLRQAVDQ WKEETGYGFS
LYSTPSENLC DRFCRLDTAE FGVVPGVTDK GYYTNSFHLD VEKKVNPYDK IDFEAPYPPL
ANGGFICYGE YPNIQHNLKA LEDVWDYSYQ HVPYYGTNTP IDECYECGFT GEFECTSKGF
TCPKCGNHDA SRVSVTRRVC GYLGSPDARP FNAGKQEEVK RRVKHLGNGQ IG
Length

712

Mol. Wt

80.023 kDa

pI

6.8 (calculated)

Extinction coefficient

80,680 - 82,680 (calc based on 32 Y, 6 W, and 16 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 References

Domain

3..90

PF03477 ATP cone domain

PMID:19920124[8]

Domain

581..687

PF01228 Glycine radical

PMID:19920124[8]

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

Structures

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

Models

View models at:

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Structure figures

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Notes

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

NCBI (Protein) (EcoliWiki Page)

GI:16132060

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948755

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013865

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P28903

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11417

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11417

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948755

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001382

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1388

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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 2.3 2.4 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 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 Garriga, X et al. (1996) nrdD and nrdG genes are essential for strict anaerobic growth of Escherichia coli. Biochem. Biophys. Res. Commun. 229 189-92 PubMed
  6. ↑ Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  7. ↑ 7.0 7.1 7.2 7.3 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  8. ↑ 8.0 8.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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