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Standard Name	ribA
Gene Synonym(s)	ECK1272, b1277, JW1269^[1], JW1269
Product Desc.	GTP cyclohydrolase II^[2]^[3]; Component of GTP cyclohydrolase II^[2]^[3] GTP cyclohydrolase II, riboflavin biosynthesis^[4]
Product Synonyms(s)	GTP cyclohydrolase II^[1], B1277^[2]^[1], RibA^[2]^[1] , ECK1272, JW1269, b1277
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ribA^[2]
Regulation/Activity
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Notes

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Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	ribA
Mnemonic	Riboflavin
Synonyms	ECK1272, b1277, JW1269^[1], JW1269
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	28.81 minutes	MG1655: 1337184..1336594 <gbrowseImage> name=NC_000913:1336594..1337184 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1337532..1336942 <gbrowseImage> name=NC_012967:1336942..1337532 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1227443..1228033 <gbrowseImage> name=NC_012759:1227443..1228033 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1340874..1340284 <gbrowseImage> name=NC_007779:1340284..1340874 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1426580..1425990 <gbrowseImage> name=NC_010473:1425990..1426580 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
Coding Start (SO:0000323)	MG1655	1336594	Edman degradation	PMID:8320220
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	AA change(s)	Phenotype: Description	Availability	Comments
ribAC54S	C54S	Loss of zinc binding. Loss of ring- opening activity. Can still remove phosphate from GTP		seeded from UniProt:P0A7I7
ribAC65S	C65S	Loss of zinc binding. Loss of ring- opening activity. Can still remove phosphate from GTP		seeded from UniProt:P0A7I7
ribAC67S	C67S	Loss of zinc binding. Loss of ring- opening activity. Can still remove phosphate from GTP		seeded from UniProt:P0A7I7
ribA13::Tn5			CGSC:9036
ribA18::Tn5			CGSC:9034
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW1269	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCAGCTTAAACGTGTGGCAGA Primer 2:CCTTTGTTCAGCAAATGGCCCAT
18B6	Kohara Phage	Genobase	PMID:3038334
trpC83::Tn10	Linked marker	CAG18455 = CGSC7371^[5]	est. P1 cotransduction: 50% ^[6] Synonyms:trpB83::Tn10
zcj-233::Tn10	Linked marker	CAG12028 = CGSC7373^[5]	est. P1 cotransduction: 28% ^[6] Synonyms:zci-233::Tn10
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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	EcoCyc:EG11331	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11331	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001302	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945763	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1307	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004285	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

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

Standard name	RibA
Synonyms	GTP cyclohydrolase II^[1], B1277^[2]^[1], RibA^[2]^[1] , ECK1272, JW1269, b1277
Product description	GTP cyclohydrolase II^[2]^[3]; Component of GTP cyclohydrolase II^[2]^[3] GTP cyclohydrolase II, riboflavin biosynthesis^[4]
EC number (for enzymes)	3.5.4.25^[1]
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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: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
	GO:0003935	GTP cyclohydrolase II activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00179	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003935	GTP cyclohydrolase II activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000926	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003935	GTP cyclohydrolase II activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:3.5.4.25	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005525	GTP binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0342	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00179	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:0009231	riboflavin biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00179	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009231	riboflavin biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000926	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
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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 GTP cyclohydrolase II	could be indirect
Protein	pyrF		PMID:16606699	Experiment(s):EBI-1139440, EBI-1139447
Protein	rrmJ		PMID:16606699	Experiment(s):EBI-1139440
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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 MQLKRVAEAK LPTPWGDFLM VGFEELATGH DHVALVYGDI SGHTPVLARV HSECLTGDAL FSLRCDCGFQ LEAALTQIAE EGRGILLYHR QEGRNIGLLN KIRAYALQDQ GYDTVEANHQ LGFAADERDF TLCADMFKLL GVNEVRLLTN NPKKVEILTE AGINIVERVP LIVGRNPNNE HYLDTKAEKM GHLLNK
Length	196
Mol. Wt	21.835 kDa
pI	5.9 (calculated)
Extinction coefficient	12,950 - 13,450 (calc based on 5 Y, 1 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	References
Domain	3..171	PF00925 GTP cyclohydrolase II		PMID:19920124
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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=ribA 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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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:16129238	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945763	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004285	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A7I7	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11331	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11331	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945763	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001302	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1307	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MG1655	2328	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	563	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	1161	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)
ribA
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:1337164..1337204 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b1277 (EcoliWiki Page)	NCBI GEO profiles for ribA
microarray	GenExpDB:b1277 (EcoliWiki Page)	Summary of data for ribA from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (1337095..1337369) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ09; Well:E4^[7]
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Notes

Accessions Related to ribA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11331	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1307	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1277
EcoGene	EcoGene:EG11331	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001302	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004285	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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

Organism	Homologs (Statistics)	Comments
Arabidopsis thaliana	AT5G59750 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q6L506 (score: 1.000; bootstrap: 100%) Q84PC2 (score: 0.833)	From Inparanoid:20070104
Saccharomyces cerevisiae	YBL033C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAP27G119c (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Shigella flexneri	RIBA	From SHIGELLACYC
E. coli O157	RIBA	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00925 GTP cyclohydrolase II
Superfamily (EcoliWiki Page)	SUPERFAMILY:142695
EcoCyc	EcoCyc:EG11331	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11331	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001302	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1307	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004285	Escherichia coli str. K-12 substr. MG1655
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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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 ^1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

ribA:On One Page

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to ribA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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