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leuB:On One Page

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Gene Name	leuB (synonyms: ECK0075, b0073, JW5807)^[1]
Product(s)	LeuB product^[1]: 3-isopropylmalate dehydrogenase product, B0073 product
Description	LeuB^[2]^[3] Component of 3-isopropylmalate dehydrogenase^[2]
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): leuLABCD^[2], OP00249, leu, leuABCD
Regulation/Activity
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Notes

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Gene

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Nomenclature

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Standard name	leuB
Mnemonic
Synonyms	ECK0075, b0073, JW5807^[1]
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Notes

Location(s) and DNA Sequence

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Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	1.74 minutes	MG1655: 81958..80867	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 81958..80867	GBrowse(W3110)	FASTA Dump
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Strain

Map location

Genome coordinates

Genome browsers

Sequence links

MG1655

1.74 minutes

MG1655: 81958..80867
gbrowse_img.php?coord=79867..82958&genome=ecoli&name=MG1655&trackset=0&width=300&.png

EcoCyc

GBrowse(MG1655)

W3110

W3110: 81958..80867
gbrowse_img.php?coord=79867..82958&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

GBrowse(W3110)

FASTA Dump

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Notes

Sequence Features

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Feature type	Location	Description
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Alleles and Phenotypes

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Allele	Nt change(s)	AA change(s)	Reference	Availability	Comments
ΔleuB (Keio:JW5807)	deletion	deletion	PMID:16738554^[4]	Shigen
leuB6(Am)				CGSC:4494	amber (UAG) mutation
leuB401				CGSC:6568
leuB61				CGSC:6570
leuB19				CGSC:8331
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Notes

Genetic Resources

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Resource	Resource Type	Source	Notes/Reference
JW5807	Plasmid clone	Shigen	PMID:16769691^[5] Status:Clone OK Primer 1:GCCTCGAAGAATTACCATATTGC Primer 2:CCaACCCCTTCTGCTACATAGCG
carB96::Tn10	Linked marker	CAG12093 = CGSC7322^[6]	est. P1 cotransduction: 11% ^[7] Synonyms:car-96::Tn10
leuO3051::Tn10	Linked marker	CAG12095 = CGSC7324^[6]	est. P1 cotransduction: 92% ^[7] Synonyms:zab-3051::Tn10 The start of leuO was reannotated by Riley et al. (2006).
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG11577
EchoBASE (EcoliWiki Page)	EchoBASE:EB1537
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0073
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C0090
EcoGene (EcoliWiki Page)	EcoGene:EG11577
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:LEUB
CGSC (EcoliWiki Page)	CGSC:571
ASAP (EcoliWikiPage)	ASAP:ABE-0000265
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Links

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Name	URL	Comments
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Product(s)

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Nomenclature

Standard name	LeuB product
Synonyms	3-isopropylmalate dehydrogenase product^[1], B0073 product^[2]^[1], LeuB product^[2]^[1]
Product description	LeuB^[2]^[3]; Component of ; 3-isopropylmalate dehydrogenase^[2]^[3]
EC number (for enzymes)	1.1.1.85^[1]
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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:0003862	3-isopropylmalate dehydrogenase activity	PMID:9003442^[8]	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0009098	leucine biosynthetic process	PMID:9003442^[8]	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0000287	magnesium ion binding	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0003862	3-isopropylmalate dehydrogenase activity	GO_REF:0000002 GO_REF:0000003 GO_REF:0000020	IEA: Inferred from Electronic Annotation	InterPro:IPR004429 EC:1.1.1.85 HAMAP:MF_01033	F	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0005737	cytoplasm	GO_REF:0000002 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR004429 SP_KW:KW-0963	C	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0009098	leucine biosynthetic process	GO_REF:0000002 GO_REF:0000004 GO_REF:0000020	IEA: Inferred from Electronic Annotation	InterPro:IPR004429 SP_KW:KW-0432 HAMAP:MF_01033	P	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0030145	manganese ion binding	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0464	F	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0046872	metal ion binding	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	F	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0009098	leucine biosynthetic process	PMID:9003442^[8]	IDA		P	Seeded from EcoCyc 11.1^[3].	required fields missing
	GO:0003862	3-isopropylmalate dehydrogenase activity	PMID:9003442^[8]	IDA		F	Seeded from EcoCyc 11.1^[3].	required fields missing
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Interactions

Partner Type	Partner	Notes	References
Protein	Subunits of 3-isopropylmalate dehydrogenase	could be indirect
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Notes

Localization

Compartment	Description	Evidence	Notes
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Notes

Structure and Physical Properties

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Physical Properties

Sequence	at EcoCyc MMSKNYHIAV LPGDGIGPEV MTQALKVLDA VRNRFAMRIT TSHYDVGGAA IDNHGQPLPP ATVEGCEQAD AVLFGSVGGP KWEHLPPDQQ PERGALLPLR KHFKLFSNLR PAKLYQGLEA FCPLRADIAA NGFDILCVRE LTGGIYFGQP KGREGSGQYE KAFDTEVYHR FEIERIARIA FESARKRRHK VTSIDKANVL QSSILWREIV NEIATEYPDV ELAHMYIDNA TMQLIKDPSQ FDVLLCSNLF GDILSDECAM ITGSMGMLPS ASLNEQGFGL YEPAGGSAPD IAGKNIANPI AQILSLALLL RYSLDADDAA CAIERAINRA LEEGIRTGDL ARGAAAVSTD EMGDIIARYV AEGV
Mol. Wt	39.52 kDa (calc) ^[2]
pI
Extinction coefficient	27390 - 28140 (calc based on 11 Y, 2 W, and 6 C residues)
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Domains/Motifs/Modification Sites

Type	Residues	Description	Notes
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Structure

Structures	Representative Escherichia coli structure: 1CM7\|A 1-363 of 364 residues (E-value: 2.0e-194) (Percent Identity: 100.00) Representative homolog: 3BLW\|B (Saccharomyces cerevisiae) 91-345 of 364 residues (E-value: 1.1e-37) (Percent Identity: 34.07) View all other structures.
Models	View models at: EcoliPredict ModBase PSI-PRED Protein Quaternary Structure (PQS) Genomes TO Protein (GTOP)
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Structures

Representative Escherichia coli structure:
1CM7|A
1-363 of 364 residues (E-value: 2.0e-194) (Percent Identity: 100.00)
Representative homolog:
3BLW|B (Saccharomyces cerevisiae)
91-345 of 364 residues (E-value: 1.1e-37) (Percent Identity: 34.07)
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Models

View models at:

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Notes

Gene Product Resources

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Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:3-ISOPROPYLMALDEHYDROG-MONOMER
UniProt (EcoliWiki Page)	UniProt:P30125
PFAM (EcoliWiki Page)	PFAM:PF00180
RefSeq (EcoliWiki Page)	RefSeq:NP_414615
ModBase (EcoliWiki Page)	ModBase:P30125
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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.

Transcription and Transcriptional Regulation

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Transcription unit(s)
leuLABCD
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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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gbrowse_img.php?coord=81938..81978&genome=ecoli&name=MG1655&trackset=Genes_unlabeled+DNA_unlabeled+flip&width=400&.png
This picture shows the sequence around the N-terminus.

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

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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Mutations Affecting Expression

Allele Name	Mutation	Phenotype	Reference
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Expression Studies

Type	Reference	Notes
microarray	EcoliGenExpDB:b0073 (EcoliWiki Page)	Summary of data for leuB from multiple microarray studies
microarray	GEO Profiles:b0073 (EcoliWiki Page)	NCBI GEO profiles for leuB
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Expression Resources

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to leuB Expression

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG11577
EchoBASE (EcoliWiki Page)	EchoBASE:EB1537
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0073
EcoGene (EcoliWiki Page)	EcoGene:EG11577
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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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Organism	Homologs (Statistics)	Comments
Arabidopsis thaliana	AT1G80560 (score: 1.000; bootstrap: 100%) AT1G31180 (score: 0.761) AT5G14200 (score: 0.756)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00036287 (score: 1.000; bootstrap: 100%) WBGene00026699 (score: 0.257) WBGene00037537 (score: 0.253)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00007993 (score: 1.000; bootstrap: 100%) WBGene00016266 (score: 0.262) WBGene00009440 (score: 0.252)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000015535 (score: 1.000; bootstrap: 100%) ENSMMUP00000028091 (score: 0.212)	From Inparanoid:20070104
Oryza gramene	Q6AT60 (score: 1.000; bootstrap: 100%) Q7Y096 (score: 0.994)	From Inparanoid:20070104
Saccharomyces cerevisiae	YCL018W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC1A42c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000014804 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Shigella flexneri	LEUB	From SHIGELLACYC
E. coli O157	LEUB	From ECOO157CYC
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Notes

Families

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Database	Accession	Notes
PFAM (EcoliWiki Page)	PFAM:PF00180
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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 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 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 ^3.4 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ Baba T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008 PubMed EcoliWiki page
↑ Kitagawa M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (A Complete Set of E. coli K-12 ORF Archive): Unique Resources for Biological Research. DNA Res 12: 291-9 PubMed EcoliWiki page
↑ ^6.0 ^6.1 CGSC: The Coli Genetics Stock Center
↑ ^7.0 ^7.1 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).
↑ ^8.0 ^8.1 ^8.2 ^8.3 Wallon G et al. (1997) Purification, catalytic properties and thermostability of 3-isopropylmalate dehydrogenase from Escherichia coli. Biochim Biophys Acta 1337: 105-12 PubMed EcoliWiki page
↑ ^9.0 ^9.1 ^9.2 ^9.3 ^9.4 ^9.5 ^9.6 ^9.7 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

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Retrieved from "http://ecoliwiki.net/colipedia/index.php/leuB:On_One_Page"

leuB:On One Page

From EcoliWiki

Quickview

Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Categories

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Categories

Expression

Overview

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to leuB Expression

Notes

Links

Categories

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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