ribD: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

RibD

Synonyms

fused diaminohydroxyphosphoribosylaminopyrimidine deaminase[1], 5-amino-6-(5-phosphoribosylamino) uracil reductase[1], B0414[2][1], RibG[2][1], RibD[2][1] , ECK0408, JW0404, ribG, ybaE, b0414

Product description

Bifunctional enzyme for second and third steps in riboflavin biosynthesis; 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate deaminase; ribosyl reductase[3]

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: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:IPR016192

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:0008703

5-amino-6-(5-phosphoribosylamino)uracil reductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002734

F

Seeded from EcoCyc (v14.0)

complete

GO:0008703

5-amino-6-(5-phosphoribosylamino)uracil reductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004794

F

Seeded from EcoCyc (v14.0)

complete

GO:0008703

5-amino-6-(5-phosphoribosylamino)uracil reductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011549

F

Seeded from EcoCyc (v14.0)

complete

GO:0008703

5-amino-6-(5-phosphoribosylamino)uracil reductase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.1.1.193

F

Seeded from EcoCyc (v14.0)

complete

GO:0008835

diaminohydroxyphosphoribosylaminopyrimidine deaminase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004794

F

Seeded from EcoCyc (v14.0)

complete

GO:0008835

diaminohydroxyphosphoribosylaminopyrimidine deaminase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.5.4.26

F

Seeded from EcoCyc (v14.0)

complete

GO:0009231

riboflavin biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002734

P

Seeded from EcoCyc (v14.0)

complete

GO:0009231

riboflavin biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004794

P

Seeded from EcoCyc (v14.0)

complete

GO:0009231

riboflavin biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011549

P

Seeded from EcoCyc (v14.0)

complete

GO:0009231

riboflavin biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0686

P

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:0050661

NADP or NADPH binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011549

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004794

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

fruB

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

hupA

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

groL

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

pbpC

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

ribH

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

rplC

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

rplD

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

rplE

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

rplS

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

rplU

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

rpsB

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

rpsD

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

rpsG

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

yciI

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

accB

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

accC

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

accD

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

agaR

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

ynfD

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

cvpA

PMID:15690043[4]

Experiment(s):EBI-894235

Protein

hemG

PMID:16606699[5]

Experiment(s):EBI-1136506

Protein

nadE

PMID:16606699[5]

Experiment(s):EBI-1136506

Protein

fur

PMID:16606699[5]

Experiment(s):EBI-1136506

Protein

groL

PMID:16606699[5]

Experiment(s):EBI-1136506

Protein

groL

PMID:19402753[6]

LCMS(ID Probability):99.6

Protein

ribE

PMID:19402753[6]

LCMS(ID Probability):99.0

Protein

accD

PMID:19402753[6]

LCMS(ID Probability):99.0

Protein

accC

PMID:19402753[6]

LCMS(ID Probability):99.0

Protein

accB

PMID:19402753[6]

LCMS(ID Probability):99.0

Protein

agaR

PMID:19402753[6]

LCMS(ID Probability):99.0

Protein

pbpC

PMID:19402753[6]

LCMS(ID Probability):99.0

Protein

yciI

PMID:19402753[6]

LCMS(ID Probability):99.0

Protein

fruB

PMID:19402753[6]

LCMS(ID Probability):99.0

Protein

ynfD

PMID:19402753[6]

LCMS(ID Probability):99.0

Protein

cvpA

PMID:19402753[6]

LCMS(ID Probability):99.0

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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 

MQDEYYMARA LKLAQRGRFT THPNPNVGCV IVKDGEIVGE GYHQRAGEPH AEVHALRMAG
EKAKGATAYV TLEPCSHHGR TPPCCDALIA AGVARVVASM QDPNPQVAGR GLYRLQQAGI
DVSHGLMMSE AEQLNKGFLK RMRTGFPYIQ LKLGASLDGR TAMASGESQW ITSPQARRDV
QLLRAQSHAI LTSSATVLAD DPALTVRWSE LDEQTQALYP QQNLRQPIRI VIDSQNRVTP
VHRIVQQPGE TWFARTQEDS REWPETVRTL LIPEHKGHLD LVVLMMQLGK QQINSIWVEA
GPTLAGALLQ AGLVDELIVY IAPKLLGSDA RGLCTLPGLE KLADAPQFKF KEIRHVGPDV
CLHLVGA
Length

367

Mol. Wt

40.337 kDa

pI

7.6 (calculated)

Extinction coefficient

39,420 - 40,170 (calc based on 8 Y, 5 W, and 6 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

1..100

PF00383 Cytidine and deoxycytidylate deaminase zinc-binding region

PMID:19920124[7]

Domain

147..362

PF01872 RibD C-terminal domain

PMID:19920124[7]

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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=ribD 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:16128399

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945620

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001441

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P25539

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11321

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11321

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945620

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001292

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1297

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 1.5 1.6 1.7 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. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  4. ↑ 4.00 4.01 4.02 4.03 4.04 4.05 4.06 4.07 4.08 4.09 4.10 4.11 4.12 4.13 4.14 4.15 4.16 4.17 4.18 4.19 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  5. ↑ 5.0 5.1 5.2 5.3 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  6. ↑ 6.00 6.01 6.02 6.03 6.04 6.05 6.06 6.07 6.08 6.09 6.10 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  7. ↑ 7.0 7.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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