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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	ghrB
Gene Synonym(s)	tiaE, ECK3540, b3553, JW5656, tkrA, yiaE^[1]^[2], yiaE
Product Desc.	YiaE^[2]; GhrB^[3] Glyoxylate/hydroxypyruvate reductase; 2-ketogluconate reductase; activity higher on hydroxypyruvate than glyoxylate^[4]
Product Synonyms(s)	2-keto-D-gluconate reductase (glyoxalate reductase) (2-ketoaldonate reductase)^[1], B3553^[2]^[1], TkrA^[2]^[1], GhrB^[2]^[1], YiaE^[2]^[1] , ECK3540, JW5656, tkrA, yiaE, b3553
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): tiaE^[2]
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

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AFMB Structural Genomics target No. 33 (http://afmb.cnrs-mrs.fr/article171.html).^[4]

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	ghrB
Mnemonic	Glyoxylate/Hydroxypyruvate Reductase
Synonyms	tiaE, ECK3540, b3553, JW5656, tkrA, yiaE^[1]^[2], yiaE
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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	80.08 minutes	MG1655: 3715333..3716307 <gbrowseImage> name=NC_000913:3715333..3716307 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3647768..3648742 <gbrowseImage> name=NC_012967:3647768..3648742 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3603659..3604633 <gbrowseImage> name=NC_012759:3603659..3604633 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3923105..3922131 <gbrowseImage> name=NC_007779:3922131..3923105 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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	3715333	Edman degradation	PMID:9298646 PMID:12639950
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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	Nt change(s)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
yiaE::Tn5KAN-I-SceI (FB21276)	Insertion at nt 392 in Plus orientation				PMID:15262929	E. coli Genome Project:FB21276	contains pKD46
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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

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

9F6

Kohara Phage

Genobase

PMID:3038334

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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:EG12272	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12272	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002153	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948074	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2181	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011604	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	TiaE
Synonyms	2-keto-D-gluconate reductase (glyoxalate reductase) (2-ketoaldonate reductase)^[1], B3553^[2]^[1], TkrA^[2]^[1], GhrB^[2]^[1], YiaE^[2]^[1] , ECK3540, JW5656, tkrA, yiaE, b3553
Product description	YiaE^[2]; GhrB^[3] Glyoxylate/hydroxypyruvate reductase; 2-ketogluconate reductase; activity higher on hydroxypyruvate than glyoxylate^[4]
EC number (for enzymes)	1.1.1.79^[1] 1.1.1.215^[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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01667	C	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006139	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008873	gluconate 2-dehydrogenase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.1.1.215	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006139	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006140	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016618	hydroxypyruvate reductase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01667	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016618	hydroxypyruvate reductase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.1.1.81	F	Seeded from EcoCyc (v14.0)	complete
	GO:0019521	D-gluconate metabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0311	P	Seeded from EcoCyc (v14.0)	complete
	GO:0030267	glyoxylate reductase (NADP) activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01667	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030267	glyoxylate reductase (NADP) activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.1.1.79	F	Seeded from EcoCyc (v14.0)	complete
	GO:0048037	cofactor binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006140	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051287	NAD or NADH binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006139	F	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	pgm		PMID:15690043	Experiment(s):EBI-882509
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</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
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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 MERSMKPSVI LYKALPDDLL QRLQEHFTVH QVANLSPQTV EQNAAIFAEA EGLLGSNENV NAALLEKMPK LRATSTISVG YDNFDVDALT ARKILLMHTP TVLTETVADT LMALVLSTAR RVVEVAERVK AGEWTASIGP DWYGTDVHHK TLGIVGMGRI GMALAQRAHF GFNMPILYNA RRHHKEAEER FNARYCDLDT LLQESDFVCL ILPLTDETHH LFGAEQFAKM KSSAIFINAG RGPVVDENAL IAALQKGEIH AAGLDVFEQE PLSVDSPLLS MANVVAVPHI GSATHETRYG MAACAVDNLI DALQGKVEKN CVNPHVAD
Length	328
Mol. Wt	35.898 kDa
pI	5.7 (calculated)
Extinction coefficient	19,940 - 20,440 (calc based on 6 Y, 2 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	References
Domain	5..319	PF00389 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain	PMID:19920124
Domain	108..287	PF02826 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain	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=ghrB taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

Structure figures

</protect>

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:90111614	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948074	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011604	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P37666	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12272	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12272	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948074	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002153	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2181	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	Notes	Reference(s)
Protein	Ecoli K-12	53.84+/-0.333	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
Protein	E. coli K-12 MG1655	2255	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	1988	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	1774	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)
tiaE
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Figure courtesy of RegulonDB

</protect>

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_000913:3715313..3715353 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

</protect>

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:b3553 (EcoliWiki Page)	NCBI GEO profiles for ghrB
microarray	GenExpDB:b3553 (EcoliWiki Page)	Summary of data for ghrB 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
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Notes

Accessions Related to ghrB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12272	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2181	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3553
EcoGene	EcoGene:EG12272	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002153	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011604	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
Anopheles gambiae	ENSANGP00000021023 (score: 1.000; bootstrap: 99%) ENSANGP00000021059 (score: 0.327) ENSANGP00000021069 (score: 0.161) ENSANGP00000011670 (score: 0.109)	From Inparanoid:20070104
Arabidopsis thaliana	AT1G79870 (score: 1.000; bootstrap: 65%) AT1G12550 (score: 0.266) AT2G45630 (score: 0.202)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000025697 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000003445 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000002692 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040724-230 (score: 1.000; bootstrap: 52%) ZDB-CDNA-050522-95 (score: 1.000; bootstrap: 52%) ZDB-CDNA-040425-2787 (score: 0.527) ZDB-GENE-040426-1847 (score: 0.527)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0231445 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0032889 (score: 1.000; bootstrap: 100%) FBgn0051674 (score: 0.546) FBgn0051673 (score: 0.295) FBgn0037370 (score: 0.161)	From Inparanoid:20070104
Drosophila pseudoobscura	GA21708-PA (score: 1.000; bootstrap: 100%) GA16384-PA (score: 0.354) GA11580-PA (score: 0.160)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000008696 (score: 1.000; bootstrap: 52%)	From Inparanoid:20070104
Homo sapiens	ENSP00000313432 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000023525 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000014965 (score: 1.000; bootstrap: 75%)	From Inparanoid:20070104
Mus musculus	MGI:1923488 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q6ZAA5 (score: 1.000; bootstrap: 55%) Q7XMP6 (score: 0.670) Q67W99 (score: 0.658)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000035821 (score: 1.000; bootstrap: 97%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000017111 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YNL274C (score: 1.000; bootstrap: 98%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPACUNK40 (score: 1.000; bootstrap: 100%) SPBC17737c (score: 0.063)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000144676 (score: 1.000; bootstrap: 75%) NEWSINFRUP00000149326 (score: 0.515)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00026561001 (score: 1.000; bootstrap: 69%) GSTENP00033054001 (score: 0.497)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000012971 (score: 1.000; bootstrap: 92%)	From Inparanoid:20070104
Shigella flexneri	YIAE	From SHIGELLACYC
E. coli O157	YIAE	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)	PF02826 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
Pfam (EcoliWiki Page)	PF00389 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:51735
Superfamily (EcoliWiki Page)	SUPERFAMILY:52283
Panther (EcoliWiki Page)	PTHR10996:SF27
EcoCyc	EcoCyc:EG12272	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12272	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002153	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2181	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011604	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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 ^1.12 ^1.13 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 ^2.11 ^2.12 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.

ghrB:On One Page

Quickview

Notes

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 ghrB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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