hybC:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

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

Standard name

HybC

Synonyms

hydrogenase 2, large subunit[1], B2994[2][1], HybC[2][1] , ECK2988, JW2962, b2994

Product description

hydrogenase 2, large subunit[2][3];

Component of hydrogenase 2[2][3]

Hydrogenase 2 [Ni Fe] large subunit, periplasmic[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:0030288

outer membrane-bounded periplasmic space

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

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:0008901

ferredoxin hydrogenase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001501

F

Seeded from EcoCyc (v14.0)

complete

GO:0008901

ferredoxin hydrogenase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018194

F

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc (v14.0)

complete

GO:0016151

nickel ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001501

F

Seeded from EcoCyc (v14.0)

complete

GO:0016151

nickel ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018194

F

Seeded from EcoCyc (v14.0)

complete

GO:0016151

nickel ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0533

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:0019898

extrinsic to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9903

C

Seeded from EcoCyc (v14.0)

complete

GO:0033748

hydrogenase (acceptor) activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.12.99.6

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

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001501

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018194

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

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

Subunits of hydrogenase 2

could be indirect

Protein

rpsB

PMID:16606699[5]

Experiment(s):EBI-1144520

Protein

nadE

PMID:16606699[5]

Experiment(s):EBI-1144520

Protein

pepQ

PMID:15690043[6]

Experiment(s):EBI-882543

Protein

tufA

PMID:15690043[6]

Experiment(s):EBI-882543, EBI-889363

Protein

rpsN

PMID:15690043[6]

Experiment(s):EBI-889363

Protein

rplL

PMID:15690043[6]

Experiment(s):EBI-889363

Protein

rplV

PMID:15690043[6]

Experiment(s):EBI-889363

Protein

rpmB

PMID:15690043[6]

Experiment(s):EBI-889363

Protein

rpsB

PMID:15690043[6]

Experiment(s):EBI-889363

Protein

rpsJ

PMID:15690043[6]

Experiment(s):EBI-889363

Protein

rpsJ

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rplL

PMID:19402753[7]

LCMS(ID Probability):99.6

</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

Periplasm

PMID:9738917[8]

EchoLocation:hybC


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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

MSQRITIDPV TRIEGHLRID CEIENGVVSK AWASGTMWRG MEEIVKNRDP RDAWMIVQRI
CGVCTTTHAL SSVRAAESAL NIDVPVNAQY IRNIILAAHT THDHIVHFYQ LSALDWVDIT
SALQADPTKA SEMLKGVSTW HLNSPEEFTK VQNKIKDLVA SGQLGIFANG YWGHPAMKLP
PEVNLIAVAH YLQALECQRD ANRVVALLGG KTPHIQNLAV GGVANPINLD GLGVLNLERL
MYIKSFIDKL SDFVEQVYKV DTAVIAAFYP EWLTRGKGAV NYLSVPEFPT DSKNGSFLFP
GGYIENADLS SYRPITSHSD EYLIKGIQES AKHSWYKDEA PQAPWEGTTI PAYDGWSDDG
KYSWVKSPTF YGKTVEVGPL ANMLVKLAAG RESTQNKLNE IVAIYQKLTG NTLEVAQLHS
TLGRIIGRTV HCCELQDILQ NQYSALITNI GKGDHTTFVK PNIPATGEFK GVGFLEAPRG
MLSHWMVIKD GIISNYQAVV PSTWNSGPRN FNDDVGPYEQ SLVGTPVADP NKPLEVVRTI
HSFDPCMACA VHVVDADGNE VVSVKVL
Length

567

Mol. Wt

62.49 kDa

pI

6.2 (calculated)

Extinction coefficient

99,810 - 100,810 (calc based on 19 Y, 13 W, and 8 C residues)


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

Initiator Methionine

1

Removed

UniProt:P0ACE0

Domain

39..552

PF00374 Nickel-dependent hydrogenase

PMID:19920124[9]

<motif_map/>

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

Structures

<beststructure> gene=hybC taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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</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:16130894

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945182

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009828

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0ACE0

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11801

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11801

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945182

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001735

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1749

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. 1.0 1.1 1.2 1.3 1.4 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. 2.0 2.1 2.2 2.3 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. 5.0 5.1 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  6. 6.0 6.1 6.2 6.3 6.4 6.5 6.6 6.7 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  7. 7.0 7.1 7.2 7.3 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  8. Sargent, F et al. (1998) Reassignment of the gene encoding the Escherichia coli hydrogenase 2 small subunit--identification of a soluble precursor of the small subunit in a hypB mutant. Eur. J. Biochem. 255 746-54 PubMed
  9. Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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