ispB:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
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octaprenyl diphosphate synthase<ref name='LIB:Riley_2006'/>, B3187<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Cel<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YhbD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, IspB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''octaprenyl diphosphate synthase<ref name='LIB:Riley_2006'/>, B3187<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Cel<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YhbD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, IspB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , cel, ECK3176, JW3154, yhbD, b3187''
|-
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.- 2.5.1.-]<ref name='LIB:Riley_2006'/>
* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.- 2.5.1.-]<ref name='LIB:Riley_2006'/>


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!|Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-  
|-  
|
|


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GO:0004659
GO:0005737
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|
prenyltransferase activity
cytoplasm
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PMID:11825609
 
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IDA: Inferred from Direct Assay
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|


|
F
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
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complete
|-
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|


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GO:0005515
C
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protein binding
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PMID:16606699
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IPI: Inferred from Physical Interaction
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UniProtKB:P60422
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F
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
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complete
|-
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GO:0005737
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cytoplasm
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|
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C  
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Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
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required fields missing 
Missing: evidence, reference
|-  
|-  
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|
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GO:0008299
GO:0000287
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isoprenoid biosynthetic process
magnesium ion binding
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GO_REF:0000002<br />GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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InterPro:IPR000092<br />SP_KW:KW-0414
SP_KW:KW-0460
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P
F
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Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
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complete  
complete  
|-
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GO:0006744
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ubiquinone biosynthetic process
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P
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Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
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required fields missing 
|-  
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GO:0016094
GO:0046872
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polyprenol biosynthetic process
metal ion binding
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PMID:11108713
GOA:spkw<br />SP_KW:GO_REF:0000004
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IMP: Inferred from Mutant Phenotype
IEA: Inferred from Electronic Annotation
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SP_KW:KW-0479
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P
F
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Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
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complete  
complete  


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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Experiment(s):EBI-1145102<br />  
Experiment(s):EBI-1145102<br />  


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!|Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


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!align=left {{table heading style}} |Name
||


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LHAMHHGTPE QAQMIRTAIE QGNGRHLLEP VLEAMNACGS LEWTRQRAEE EADKAIAALQ
LHAMHHGTPE QAQMIRTAIE QGNGRHLLEP VLEAMNACGS LEWTRQRAEE EADKAIAALQ
VLPDTPWREA LIGLAHIAVQ RDR</pre>  
VLPDTPWREA LIGLAHIAVQ RDR</pre>  
|-
!align=left {{table heading style}} |Length
||
323
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
35.22 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
35.217 kDa
|-
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!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
4.6 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
24410 - 24785 (calc based on 9 Y, 2 W, and 3 C residues)  
24,410 - 24,785 (calc based on 9 Y, 2 W, and 3 C residues)


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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
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|- {{table heading style}}
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
31..285
|
[http://pfam.janelia.org/family/PF00348 PF00348  Polyprenyl synthetase]
|
 
|
PMID:19920124


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<td>
<!-- motifs column 2-->
<motif_map/>
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<table><tr valign='top'><td>
<span id="Structure"></span><big>'''Structure'''</big>
<span id='Structure'></span><big>'''Structure'''</big><br />
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|-
|-
!align=left {{table heading style}} |Structures
!align=left {{table heading style}} |Structures
||
||
<beststructure>ispB
<beststructure>
562</beststructure>
gene=ispB
 
taxon=562,83333
</beststructure>
|-
|-
!align=left {{table heading style}} |Models
!align=left {{table heading style}} |Models
||
||
View models at:
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=ispB&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P0AD57 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=ispB&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0AD57 PSI-PRED (P0AD57)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0AD57 Genomes TO Protein (P0AD57)] (GTOP)
* [http://www.ebi.ac.uk/msd-srv/pqs/ Protein Quaternary Structure] (PQS)
* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)


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<!--Structure_notes--></protect>
</td><td></protect>
==== Structure figures ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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===Notes===
===Notes===


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!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference


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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/16131077 GI:16131077]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/NP_417654.1 GeneID:947364]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0010474
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=OPPSYN-MONOMER EcoCyc:OPPSYN-MONOMER]
[http://www.uniprot.org/uniprot/P0AD57 UniProtKB/Swiss-Prot:P0AD57]
|
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Escherichia coli str. K-12 substr. MG1655
|-
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[[EcoCyc]]
|
EcoCyc:EG10017
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoGene]]
|
|
[[uniprot:P0AD57|UniProt:P0AD57]]
EcoGene:EG10017
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[http://pfam.sanger.ac.uk/family?acc=PF00348 PFAM:PF00348]
[http://www.ncbi.nlm.nih.gov/gene?term=947364 GeneID:947364]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_417654 RefSeq:NP_417654]
RegulonDB:ECK120000015
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
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[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://salilab.org/modbase/searchbyid?databaseID=P0AD57 ModBase:P0AD57]
EchoBASE:EB0017
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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==References==
==References==
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===Categories===
===Categories===
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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0006744_!_ubiquinone biosynthetic process]][[Category:Complex:octaprenyl diphosphate synthase]]

Latest revision as of 21:00, 17 February 2015

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
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

IspB

Synonyms

octaprenyl diphosphate synthase[1], B3187[2][1], Cel[2][1], YhbD[2][1], IspB[2][1] , cel, ECK3176, JW3154, yhbD, b3187

Product description

OPPSYN[2][3];

Component of octaprenyl diphosphate synthase[3]

Octaprenyl diphosphate synthase, isoprenoid biosynthesis[4]

EC number (for enzymes)
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Notes

Function

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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:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0000287

magnesium ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

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

Subunits of octaprenyl diphosphate synthase

could be indirect

Protein

rplB

PMID:16606699[5]

Experiment(s):EBI-1145102
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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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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 

MNLEKINELT AQDMAGVNAA ILEQLNSDVQ LINQLGYYIV SGGGKRIRPM IAVLAARAVG
YEGNAHVTIA ALIEFIHTAT LLHDDVVDES DMRRGKATAN AAFGNAASVL VGDFIYTRAF
QMMTSLGSLK VLEVMSEAVN VIAEGEVLQL MNVNDPDITE ENYMRVIYSK TARLFEAAAQ
CSGILAGCTP EEEKGLQDYG RYLGTAFQLI DDLLDYNADG EQLGKNVGDD LNEGKPTLPL
LHAMHHGTPE QAQMIRTAIE QGNGRHLLEP VLEAMNACGS LEWTRQRAEE EADKAIAALQ
VLPDTPWREA LIGLAHIAVQ RDR
Length

323

Mol. Wt

35.217 kDa

pI

4.6 (calculated)

Extinction coefficient

24,410 - 24,785 (calc based on 9 Y, 2 W, and 3 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

31..285

PF00348 Polyprenyl synthetase

PMID:19920124[6]

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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=ispB taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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:16131077

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947364

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010474

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AD57

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10017

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10017

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947364

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000015

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0017

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 1.5 1.6 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 2.4 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. ↑ Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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