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Gene |

Product(s) |

Expression|

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References |

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Standard Name	gcd
Gene Synonym(s)	ECK0123, b0124, JW0120^[1], JW0120
Product Desc.	Glucose dehydrogenase (pyrroloquinoline-quinone) quinoprotein; inner membrane protein^[2]
Product Synonyms(s)	glucose dehydrogenase^[1], B0124^[3]^[1], Gcd^[3]^[1] , ECK0123, JW0120, b0124
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): gcd^[3]
Regulation/Activity
Quick Links
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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	gcd
Mnemonic	Glucose dehydrogenase
Synonyms	ECK0123, b0124, JW0120^[1], JW0120
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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	2.99 minutes	MG1655: 141225..138835 <gbrowseImage> name=NC_000913:138835..141225 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 144028..141638 <gbrowseImage> name=NC_012967:141638..144028 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 138834..141224 <gbrowseImage> name=NC_012759:138834..141224 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 141225..138835 <gbrowseImage> name=NC_007779:138835..141225 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 115329..112939 <gbrowseImage> name=NC_010473:112939..115329 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	138835	Edman degradation	PMID:8509415
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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)	Reference	Availability
gcd(del) (Keio:JW0120)	deletion	deletion	PMID:16738554	Shigen CGSC8400^[4]
gcd-1::cat			PMID:2228962	CGSC:70593
gcd(del)-742::kan			PMID:16738554	CGSC:101114
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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
JW0120	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCAATTAACAATACAGGCTC Primer 2:CCCTTCACATCATCCGGCAGCGC
4E11	Kohara Phage	Genobase	PMID:3038334
17C11	Kohara Phage	Genobase	PMID:3038334
leuO3051::Tn10	Linked marker	CAG12095 = CGSC7324^[4]	est. P1 cotransduction: 7% ^[5] Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).
zad-220::Tn10	Linked marker	CAG12025 = CGSC7326^[4]	est. P1 cotransduction: 72% ^[5]
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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:EG10369	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10369	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944830	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000362	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0364	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000433	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	Gcd
Synonyms	glucose dehydrogenase^[1], B0124^[3]^[1], Gcd^[3]^[1] , ECK0123, JW0120, b0124
Product description	Glucose dehydrogenase (pyrroloquinoline-quinone) quinoprotein; inner membrane protein^[2]
EC number (for enzymes)	1.1.5.2^[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:0000287	magnesium ion binding	PMID:12686133	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0008876	quinoprotein glucose dehydrogenase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.1.5.2	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008876	quinoprotein glucose dehydrogenase activity	PMID:8509415	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017511	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	PMID:8509415	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0016052	carbohydrate catabolic process	PMID:10359647	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0019595	non-phosphorylated glucose catabolic process	PMID:2228962	IGI: Inferred from Genetic Interaction		P	Seeded from EcoCyc (v14.0)	Missing: with/from
	GO:0030288	outer membrane-bounded periplasmic space	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001479	C	Seeded from EcoCyc (v14.0)	complete
	GO:0048039	ubiquinone binding	PMID:14612441	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001479	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017511	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR019551	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR019556	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
	GO:0070968	pyrroloquinoline quinone binding	PMID:9705344	IDA: Inferred from Direct Assay		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	References	Evidence
Protein	rmuC	PMID:16606699	Experiment(s):EBI-1135661
Protein	glpD	PMID:16606699	Experiment(s):EBI-1135661
Protein	groL	PMID:16606699	Experiment(s):EBI-1135661
Protein	zwf	PMID:16606699	Experiment(s):EBI-1135661
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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
plasma membrane	C-terminus localized to the periplasm with 5 predicted transmembrane domains	Daley et al. (2005) ^[6]
plasma membrane
Inner Membrane		PMID:8509415, PMID:8419307, PMID:8554505	EchoLocation:gcd
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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 MAINNTGSRR LLVTLTALFA ALCGLYLLIG GGWLVAIGGS WYYPIAGLVM LGVAWMLWRS KRAALWLYAA LLLGTMIWGV WEVGFDFWAL TPRSDILVFF GIWLILPFVW RRLVIPASGA VAALVVALLI SGGILTWAGF NDPQEINGTL SADATPAEAI SPVADQDWPA YGRNQEGQRF SPLKQINADN VHNLKEAWVF RTGDVKQPND PGEITNEVTP IKVGDTLYLC TAHQRLFALD AASGKEKWHY DPELKTNESF QHVTCRGVSY HEAKAETASP EVMADCPRRI ILPVNDGRLI AINAENGKLC ETFANKGVLN LQSNMPDTKP GLYEPTSPPI ITDKTIVMAG SVTDNFSTRE TSGVIRGFDV NTGELLWAFD PGAKDPNAIP SDEHTFTFNS PNSWAPAAYD AKLDLVYLPM GVTTPDIWGG NRTPEQERYA SSILALNATT GKLAWSYQTV HHDLWDMDLP AQPTLADITV NGQKVPVIYA PAKTGNIFVL DRRNGELVVP APEKPVPQGA AKGDYVTPTQ PFSELSFRPT KDLSGADMWG ATMFDQLVCR VMFHQMRYEG IFTPPSEQGT LVFPGNLGMF EWGGISVDPN REVAIANPMA LPFVSKLIPR GPGNPMEQPK DAKGTGTESG IQPQYGVPYG VTLNPFLSPF GLPCKQPAWG YISALDLKTN EVVWKKRIGT PQDSMPFPMP VPVPFNMGMP MLGGPISTAG NVLFIAATAD NYLRAYNMSN GEKLWQGRLP AGGQATPMTY EVNGKQYVVI SAGGHGSFGT KMGDYIVAYA LPDDVK
Length	796
Mol. Wt	86.748 kDa
pI	5.4 (calculated)
Extinction coefficient	169,250 - 170,125 (calc based on 25 Y, 24 W, and 7 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	225..262	PF01011 PQQ enzyme repeat	PMID:19920124
Domain	353..391	PF01011 PQQ enzyme repeat	PMID:19920124
Domain	436..469	PF01011 PQQ enzyme repeat	PMID:19920124
Domain	660..698	PF01011 PQQ enzyme repeat	PMID:19920124
Domain	721..759	PF01011 PQQ enzyme repeat	PMID:19920124
Domain	164..207	PF10527 Pyrrolo-quinoline quinone coenzyme N-terminus	PMID:19920124
Domain	404..425	PF10535 Pyrrolo-quinoline quinone coenzyme C-terminus	PMID:19920124
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<motif_map/>

Click the image to view raw output from TMHMM.

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

Structures

<beststructure> gene=gcd 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:16128117	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944830	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000433	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P15877	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10369	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10369	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944830	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000362	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0364	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 MC4100	4.67E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	582	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	415	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	457	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)
gcd
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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_000913:141205..141245 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:b0124 (EcoliWiki Page)	NCBI GEO profiles for gcd
microarray	GenExpDB:b0124 (EcoliWiki Page)	Summary of data for gcd 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 gcd Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10369	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0364	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0124
EcoGene	EcoGene:EG10369	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000362	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000433	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	GCD	From SHIGELLACYC
E. coli O157	GCD	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)	PF01011 PQQ enzyme repeat
Pfam (EcoliWiki Page)	PF01011 PQQ enzyme repeat
Pfam (EcoliWiki Page)	PF01011 PQQ enzyme repeat
Pfam (EcoliWiki Page)	PF01011 PQQ enzyme repeat
Pfam (EcoliWiki Page)	PF01011 PQQ enzyme repeat
Superfamily (EcoliWiki Page)	SUPERFAMILY:50998
Pfam (EcoliWiki Page)	PF10527 Pyrrolo-quinoline quinone coenzyme N-terminus
Pfam (EcoliWiki Page)	PF10535 Pyrrolo-quinoline quinone coenzyme C-terminus
EcoCyc	EcoCyc:EG10369	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10369	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000362	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0364	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000433	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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 CGSC: The Coli Genetics Stock Center
↑ ^5.0 ^5.1 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).
↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed

gcd: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 gcd Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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