hypB: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

HypB

Synonyms

GTP hydrolase involved in nickel liganding into hydrogenases[1], B2727[2][1], HydB[2][1], HypB[2][1] , ECK2722, hydB, hydE, JW2697, b2727

Product description

accessory protein for nickel incorporation into hydrogenase isoenzymes[2][3]

Required for metallocenter assembly in Hydrogenases 1,2,3; guanine-nucleotide-binding protein; Ni donor for Hyd-3 large subunit; homodimeric[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:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0005525

GTP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0342

F

Seeded from EcoCyc (v14.0)

complete

GO:0006461

protein complex assembly

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004392

P

Seeded from EcoCyc (v14.0)

complete

GO:0016151

nickel ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004392

F

Seeded from EcoCyc (v14.0)

complete

GO:0016151

nickel ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012202

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:0005515

protein binding

PMID:15569666[5]

IPI: Inferred from Physical Interaction

UniProtKB:P0A9K9

F

Interacts with SlyD

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

Protein

pflA

PMID:16606699[6]

Experiment(s):EBI-1143757

Protein

fur

PMID:16606699[6]

Experiment(s):EBI-1143757

Protein

matC

PMID:16606699[6]

Experiment(s):EBI-1143757

Protein

hflB

PMID:16606699[6]

Experiment(s):EBI-1143757

Protein

slyD

PMID:19402753[7]

LCMS(ID Probability):99.6 MALDI(Z-score):10.085167

Protein

yfeA

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

glrK

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

SlyD (FKBP-type peptidyl-prolyl cis-trans isomerase)

HypB was shown to directly interact with SlyD & a slyD- strain has reduced hydrogenase activity & accumulates an immature (unprocessed) form of the hydrogenase (HycE), which can be complemented by the addition of nickel to the growth medium or complemented with plasmid-borne expression of SlyD. See PMID:15569666[5]


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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 

MCTTCGCGEG NLYIEGDEHN PHSAFRSAPF APAARPKMKI TGIKAPEFTP SQTEEGDLHY
GHGEAGTHAP GMSQRRMLEV EIDVLDKNNR LAERNRARFA ARKQLVLNLV SSPGSGKTTL
LTETLMRLKD SVPCAVIEGD QQTVNDAARI RATGTPAIQV NTGKGCHLDA QMIADAAPRL
PLDDNGILFI ENVGNLVCPA SFDLGEKHKV AVLSVTEGED KPLKYPHMFA AASLMLLNKV
DLLPYLNFDV EKCIACAREV NPEIEIILIS ATSGEGMDQW LNWLETQRCA
Length

290

Mol. Wt

31.565 kDa

pI

5.5 (calculated)

Extinction coefficient

16,960 - 18,085 (calc based on 4 Y, 2 W, and 9 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

105..268

PF02492 CobW/HypB/UreG, nucleotide-binding domain

PMID:19920124[8]

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

Structures

<beststructure> gene=hypB 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:16130634

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947194

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008960

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AAN3

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10484

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10484

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947194

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000477

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0479

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 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. ↑ 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 Zhang, JW et al. (2005) A role for SlyD in the Escherichia coli hydrogenase biosynthetic pathway. J. Biol. Chem. 280 4360-6 PubMed
  6. ↑ 6.0 6.1 6.2 6.3 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  7. ↑ 7.0 7.1 7.2 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  8. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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