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On One Page

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Gene |

Product(s) |

Expression|

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Standard Name	gmm
Gene Synonym(s)	nudD, ECK2045, b2051, JW5335, wcaH, yefC^[1]^[2], yefC
Product Desc.	GDP-mannose mannosyl hydrolase; homodimeric^[3]
Product Synonyms(s)	GDP-mannose mannosyl hydrolase^[1], B2051^[4]^[1], Gmm^[4]^[1], NudD^[4]^[1], YefC^[4]^[1], WcaH^[4]^[1] , ECK2045, JW5335, nudD, wcaH, yefC, b2051
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): wzxC^[4]
Regulation/Activity
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Notes

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Nudix hydrolase.^[3]

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	gmm
Mnemonic	GDP-Mannose Mannosyl hydrolase
Synonyms	nudD, ECK2045, b2051, JW5335, wcaH, yefC^[1]^[2], yefC
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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	45.77 minutes	MG1655: 2124246..2123767 <gbrowseImage> name=NC_000913:2123767..2124246 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2058948..2059427 <gbrowseImage> name=NC_012967:2058948..2059427 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2016250..2016729 <gbrowseImage> name=NC_012759:2016250..2016729 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2128359..2127880 <gbrowseImage> name=NC_007779:2127880..2128359 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
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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
wcaH::Tn5KAN-I-SceI (FB20599)	Insertion at nt 222 in Plus orientation				PMID:15262929	E. coli Genome Project:FB20599	contains pKD46
nudDH123Q		H123Q		Increases Km for GDP-mannose 5- fold. Reduces activity 2000-fold			seeded from UniProt:P32056
nudDD21A		D21A		Increases Km for GDP-mannose 5- fold. Reduces activity 120-fold			seeded from UniProt:P32056
nudDD21N		D21N		Increases Km for GDP-mannose 9- fold. Reduces activity 400-fold			seeded from UniProt:P32056
nudDR36Q		R36Q		Increases Km for GDP-mannose 9- fold. Reduces activity 24-fold			seeded from UniProt:P32056
nudDR51K		R51K		Increases Km for GDP-mannose 40- fold. Reduces activity 10-fold			seeded from UniProt:P32056
nudDR51Q		R51Q		Increases Km for GDP-mannose 40- fold. Reduces activity 300-fold			seeded from UniProt:P32056
nudDR64Q		R64Q		Increases Km for GDP-mannose 80- fold. Reduces activity 24-fold			seeded from UniProt:P32056
nudDE69Q		E69Q		Increases Km for GDP-mannose 10- fold. Increases Km for magnesium 40-fold. Reduces activity 150-fold			seeded from UniProt:P32056
nudDH87Q		H87Q		Increases Km for GDP-mannose 4- fold. Reduces activity 200-fold			seeded from UniProt:P32056
nudDH101Q		H101Q		Increases Km for GDP-mannose 14- fold. Reduces activity 7-fold			seeded from UniProt:P32056
nudDY102F		Y102F		Increases Km for GDP-mannose 7- fold. Reduces activity 100-fold			seeded from UniProt:P32056
ΔwcaH::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
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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:
10A9	Kohara Phage	Genobase	PMID:3038334
7A3	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:EG11789	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11789	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001723	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946559	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1737	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006796	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	NudD
Synonyms	GDP-mannose mannosyl hydrolase^[1], B2051^[4]^[1], Gmm^[4]^[1], NudD^[4]^[1], YefC^[4]^[1], WcaH^[4]^[1] , ECK2045, JW5335, nudD, wcaH, yefC, b2051
Product description	GDP-mannose mannosyl hydrolase; homodimeric^[3]
EC number (for enzymes)	1.1.1.271^[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:0000287	magnesium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009103	lipopolysaccharide biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0448	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
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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 MMFLRQEDFA TVVRSTPLVS LDFIVENSRG EFLLGKRTNR PAQGYWFVPG GRVQKDETLE AAFERLTMAE LGLRLPITAG QFYGVWQHFY DDNFSGTDFT THYVVLGFRF RVSEEELLLP DEQHDDYRWL TSDALLASDN VHANSRAYFL AEKRTGVPGL
Length	160
Mol. Wt	18.404 kDa
pI	5.0 (calculated)
Extinction coefficient	25,440 (calc based on 6 Y, 3 W, and 0 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	16..152	PF00293 NUDIX 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=gmm taxon=562,83333 </beststructure>

Models

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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:90111376	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946559	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006796	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P32056	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11789	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11789	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946559	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001723	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1737	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	E. coli K-12 MG1655	0^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	2^a	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	0^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	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)
wzxC
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File:.jpg

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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_000913:2124226..2124266 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:b2051 (EcoliWiki Page)	NCBI GEO profiles for gmm
microarray	GenExpDB:b2051 (EcoliWiki Page)	Summary of data for gmm 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 gmm Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11789	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1737	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2051
EcoGene	EcoGene:EG11789	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001723	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006796	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
Shigella flexneri	WCAH	From SHIGELLACYC
E. coli O157	WCAH	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)	PF00293 NUDIX domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:55811
EcoCyc	EcoCyc:EG11789	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11789	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001723	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1737	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006796	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 ^1.14 ^1.15 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^4.00 ^4.01 ^4.02 ^4.03 ^4.04 ^4.05 ^4.06 ^4.07 ^4.08 ^4.09 ^4.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

gmm: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 gmm Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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