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Expression|

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Standard Name	hypD
Gene Synonym(s)	ECK2724, b2729, JW2699, hydF^[1], hydF
Product Desc.	protein involved in maturation of hydrogenase isoenzymes^[2]^[3] Hydrogenases 1,2,3 accessory protein; required for metallocenter assembly^[4]
Product Synonyms(s)	protein required for maturation of hydrogenases^[1], B2729^[2]^[1], HydF^[2]^[1], HypD^[2]^[1] , ECK2724, hydF, JW2699, b2729
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): hypBCDE-fhlA^[2], hypABCDE-fhlA^[2], hypBCDE^[2], hydBEF, hypABCDE^[2], OP00209
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	hypD
Mnemonic	Hydrogenase pleiotropic
Synonyms	ECK2724, b2729, JW2699, hydF^[1], hydF
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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	61.43 minutes	MG1655: 2850158..2851279 <gbrowseImage> name=NC_000913:2850158..2851279 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2746996..2748117 <gbrowseImage> name=NC_012967:2746996..2748117 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2735970..2737091 <gbrowseImage> name=NC_012759:2735970..2737091 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2850792..2851913 <gbrowseImage> name=NC_007779:2850792..2851913 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2942700..2943821 <gbrowseImage> name=NC_010473:2942700..2943821 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
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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	Comments
ΔhypD (Keio:JW2699)	deletion	deletion	PMID:16738554	Shigen CGSC10124^[5]
hypD::Tn5KAN-I-SceI (FB20912)	Insertion at nt 534 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20912	contains pKD46
ΔhypD733::kan			PMID:16738554	CGSC:101508
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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
JW2699	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCGTTTTGTTGATGAATATCG Primer 2:CCgGCTTCACTCTCCTGCTGACG
12F2	Kohara Phage	Genobase	PMID:3038334
25D2	Kohara Phage	Genobase	PMID:3038334
srlD3131::Tn10	Linked marker	CAG18642 = CGSC7423^[5]	est. P1 cotransduction: 40% ^[6] Synonyms:zfh-3131::Tn10, zfi-3131::Tn10
cysI95::Tn10	Linked marker	CAG12173 = CGSC7425^[5]	est. P1 cotransduction: 23% ^[6] Synonyms:cysC95::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:EG10486	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10486	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000479	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947189	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0481	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008965	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	HypD
Synonyms	protein required for maturation of hydrogenases^[1], B2729^[2]^[1], HydF^[2]^[1], HypD^[2]^[1] , ECK2724, hydF, JW2699, b2729
Product description	protein involved in maturation of hydrogenase isoenzymes^[2]^[3] Hydrogenases 1,2,3 accessory protein; required for metallocenter assembly^[4]
EC number (for enzymes)
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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:0046872	metal ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002780	F	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	References	Evidence
Protein	hypC	PMID:15690043	Experiment(s):EBI-885026, EBI-885054, EBI-891881, EBI-891896
Protein	groL	PMID:15690043	Experiment(s):EBI-885026
Protein	tufA	PMID:15690043	Experiment(s):EBI-885026, EBI-891881
Protein	hypE	PMID:15690043	Experiment(s):EBI-891881
Protein	yfdZ	PMID:16606699	Experiment(s):EBI-1143763
Protein	groL	PMID:16606699	Experiment(s):EBI-1143763
Protein	iscS	PMID:19402753	MALDI(Z-score):37.973859
Protein	rpmB	PMID:19402753	LCMS(ID Probability):99.6
Protein	dps	PMID:19402753	MALDI(Z-score):35.394040
Protein	clpB	PMID:19402753	MALDI(Z-score):22.303018
Protein	fusA	PMID:19402753	LCMS(ID Probability):98.5 MALDI(Z-score):28.349867
Protein	groS	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):26.229367
Protein	recA	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):29.172138
Protein	ompC	PMID:19402753	MALDI(Z-score):40.071150
Protein	tufB	PMID:19402753	MALDI(Z-score):20.729662
Protein	hybC	PMID:19402753	MALDI(Z-score):23.142744
Protein	dnaJ	PMID:19402753	MALDI(Z-score):24.656966
Protein	gatY	PMID:19402753	MALDI(Z-score):19.386141
Protein	mreB	PMID:19402753	MALDI(Z-score):35.917468
Protein	hypE	PMID:19402753	LCMS(ID Probability):99.4 MALDI(Z-score):18.500542
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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 MRFVDEYRAP EQVMQLIEHL RERASHLSYT AERPLRIMEV CGGHTHAIFK FGLDQLLPEN VEFIHGPGCP VCVLPMGRID TCVEIASHPE VIFCTFGDAM RVPGKQGSLL QAKARGADVR IVYSPMDALK LAQENPTRKV VFFGLGFETT MPTTAITLQQ AKARDVQNFY FFCQHITLIP TLRSLLEQPD NGIDAFLAPG HVSMVIGTDA YNFIASDFHR PLVVAGFEPL DLLQGVVMLV QQKIAAHSKV ENQYRRVVPD AGNLLAQQAI ADVFCVNGDS EWRGLGVIES SGVHLTPDYQ RFDAEAHFRP APQQVCDDPR ARCGEVLTGK CKPHQCPLFG NTCNPQTAFG ALMVSSEGAC AAWYQYRQQE SEA
Length	373
Mol. Wt	41.362 kDa
pI	6.2 (calculated)
Extinction coefficient	24,410 - 26,035 (calc based on 9 Y, 2 W, and 13 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	9..369	PF01924 Hydrogenase formation hypA family		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=hypD 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:16130636	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947189	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008965	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P24192	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10486	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10486	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947189	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000479	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0481	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	3.857+/-0.054	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.009366637	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	82	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	24	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	43	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)
hypBCDE-fhlA
hypABCDE-fhlA
hypBCDE
hypABCDE
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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_000913:2850138..2850178 source=MG1655 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:b2729 (EcoliWiki Page)	NCBI GEO profiles for hypD
microarray	GenExpDB:b2729 (EcoliWiki Page)	Summary of data for hypD 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 hypD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10486	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0481	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2729
EcoGene	EcoGene:EG10486	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000479	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008965	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	HYPD	From SHIGELLACYC
E. coli O157	HYPD	From ECOO157CYC
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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)	PF01924 Hydrogenase formation hypA family
EcoCyc	EcoCyc:EG10486	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10486	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000479	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0481	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008965	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)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 ^2.11 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 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 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).

hypD:On One Page

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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 hypD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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