hypD: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

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 Notes References Evidence

Protein

hypC

PMID:15690043[5]

Experiment(s):EBI-885026, EBI-885054, EBI-891881, EBI-891896

Protein

groL

PMID:15690043[5]

Experiment(s):EBI-885026

Protein

tufA

PMID:15690043[5]

Experiment(s):EBI-885026, EBI-891881

Protein

hypE

PMID:15690043[5]

Experiment(s):EBI-891881

Protein

yfdZ

PMID:16606699[6]

Experiment(s):EBI-1143763

Protein

groL

PMID:16606699[6]

Experiment(s):EBI-1143763

Protein

iscS

PMID:19402753[7]

MALDI(Z-score):37.973859

Protein

rpmB

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

dps

PMID:19402753[7]

MALDI(Z-score):35.394040

Protein

clpB

PMID:19402753[7]

MALDI(Z-score):22.303018

Protein

fusA

PMID:19402753[7]

LCMS(ID Probability):98.5 MALDI(Z-score):28.349867

Protein

groS

PMID:19402753[7]

LCMS(ID Probability):99.6 MALDI(Z-score):26.229367

Protein

recA

PMID:19402753[7]

LCMS(ID Probability):99.6 MALDI(Z-score):29.172138

Protein

ompC

PMID:19402753[7]

MALDI(Z-score):40.071150

Protein

tufB

PMID:19402753[7]

MALDI(Z-score):20.729662

Protein

hybC

PMID:19402753[7]

MALDI(Z-score):23.142744

Protein

dnaJ

PMID:19402753[7]

MALDI(Z-score):24.656966

Protein

gatY

PMID:19402753[7]

MALDI(Z-score):19.386141

Protein

mreB

PMID:19402753[7]

MALDI(Z-score):35.917468

Protein

hypE

PMID:19402753[7]

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[8]

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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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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: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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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 5.2 5.3 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  6. ↑ 6.0 6.1 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  7. ↑ 7.00 7.01 7.02 7.03 7.04 7.05 7.06 7.07 7.08 7.09 7.10 7.11 7.12 7.13 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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