pntB:On One Page

From EcoliWiki
Jump to: navigation, search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

Quickview

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

<protect>

Standard Name

pntB

Gene Synonym(s)

ECK1597, b1602, JW1594[1], JW1594

Product Desc.

pyridine nucleotide transhydrogenase, β subunit[2][3];

Component of pyridine nucleotide transhydrogenase[2][3]

Proton-translocating NAD(P) transhydrogenase, beta subunit; membrane protein[4]

Product Synonyms(s)

pyridine nucleotide transhydrogenase, beta subunit[1], B1602[2][1], PntB[2][1] , ECK1597, JW1594, b1602

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): pntAB[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]


PntAB couples the inward translocation of protons across the cytoplasmic membrane to the reduction of NADP+ by NADH[4]



Gene

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

pntB

Mnemonic

Pyridine nucleotide transhydrogenase

Synonyms

ECK1597, b1602, JW1594[1], JW1594

</protect>

Notes

Location(s) and DNA Sequence

[back to top]


<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

36.06 minutes 

MG1655: 1674384..1672996
<gbrowseImage> name=NC_000913:1672996..1674384 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1653555..1652167
<gbrowseImage> name=NC_012967:1652167..1653555 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1565055..1566443
<gbrowseImage> name=NC_012759:1565055..1566443 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1678074..1676686
<gbrowseImage> name=NC_007779:1676686..1678074 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1765345..1763957
<gbrowseImage> name=NC_010473:1763957..1765345 source=DH10B preset=GeneLocation </gbrowseImage>

</protect>

Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

1672996

Edman degradation

PMID:3525165


<protect></protect>

Notes

Alleles and Phenotypes

[back to top]


See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔpntB (Keio:JW1594)

deletion

deletion

PMID:16738554

Shigen
CGSC9355[5]

pntB::Tn5KAN-2 (FB20378)

Insertion at nt 862 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20378

contains pKD46

pntB::Tn5KAN-2 (FB20379)

Insertion at nt 862 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20379

does not contain pKD46

ΔpntB750::kan

PMID:16738554

CGSC:102392


<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

Interactor Interaction Allele Score(s) Reference(s) Accessions Notes

</protect>

Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW1594

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTCTGGAGGATTAGTTACAGC

Primer 2:CCaAGAGCTTTCAGGATTGCATC

E3F2

Kohara Phage

Genobase

PMID:3038334

11H12

Kohara Phage

Genobase

PMID:3038334

6A3

Kohara Phage

Genobase

PMID:3038334

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[5]

est. P1 cotransduction: % [6]
Synonyms:zdc-235::Tn10

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[5]

est. P1 cotransduction: % [6]
Synonyms:zdh-925::Tn10

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG10745

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10745

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000736

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946144

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0738

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005352

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



Product(s)

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

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

Standard name

PntB

Synonyms

pyridine nucleotide transhydrogenase, beta subunit[1], B1602[2][1], PntB[2][1] , ECK1597, JW1594, b1602

Product description

pyridine nucleotide transhydrogenase, β subunit[2][3];

Component of pyridine nucleotide transhydrogenase[2][3]

Proton-translocating NAD(P) transhydrogenase, beta subunit; membrane protein[4]

EC number (for enzymes)

<protect></protect>

Notes

Function

[back to top]


<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:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0997

C

Seeded from EcoCyc (v14.0)

complete

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:0008746

NAD(P) transhydrogenase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004003

F

Seeded from EcoCyc (v14.0)

complete

GO:0008750

NAD(P)+ transhydrogenase (AB-specific) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012136

F

Seeded from EcoCyc (v14.0)

complete

GO:0008750

NAD(P)+ transhydrogenase (AB-specific) activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.6.1.2

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:0016021

integral to membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012136

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0812

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9909

C

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:0050661

NADP or NADPH binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012136

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004003

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012136

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 pyridine nucleotide transhydrogenase

could be indirect


</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

plasma membrane

C-terminus localized in the cytoplasm with 9 predicted transmembrane domains

Daley et al. (2005) [7]

plasma membrane

From EcoCyc[3]


<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<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

MSGGLVTAAY IVAAILFIFS LAGLSKHETS RQGNNFGIAG MAIALIATIF GPDTGNVGWI
LLAMVIGGAI GIRLAKKVEM TEMPELVAIL HSFVGLAAVL VGFNSYLHHD AGMAPILVNI
HLTEVFLGIF IGAVTFTGSV VAFGKLCGKI SSKPLMLPNR HKMNLAALVV SFLLLIVFVR
TDSVGLQVLA LLIMTAIALV FGWHLVASIG GADMPVVVSM LNSYSGWAAA AAGFMLSNDL
LIVTGALVGS SGAILSYIMC KAMNRSFISV IAGGFGTDGS STGDDQEVGE HREITAEETA
ELLKNSHSVI ITPGYGMAVA QAQYPVAEIT EKLRARGINV RFGIHPVAGR LPGHMNVLLA
EAKVPYDIVL EMDEINDDFA DTDTVLVIGA NDTVNPAAQD DPKSPIAGMP VLEVWKAQNV
IVFKRSMNTG YAGVQNPLFF KENTHMLFGD AKASVDAILK AL
Length

462

Mol. Wt

48.723 kDa

pI

6.1 (calculated)

Extinction coefficient

33,920 - 34,170 (calc based on 8 Y, 4 W, and 2 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

Domain

4..462

PF02233 NAD(P) transhydrogenase beta subunit

PMID:19920124

<motif_map/>

tmhmm.php?gene=pntB&show=pic&.jpg
Click the image to view raw output from TMHMM.

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

Structures

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

Models

View models at:

</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


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

Resource type Source Notes/Reference

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16129560

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946144

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005352

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AB67

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10745

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10745

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946144

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000736

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0738

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]




Expression

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]


See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MC4100

1.98E+02

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

E. coli K-12 MG1655

1164

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

2712

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

473

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Notes

Transcription and Transcriptional Regulation

[back to top]


<protect>

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

Transcription unit(s)

pntAB

Figure courtesy of RegulonDB

</protect>

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

[back to top]


<protect><gbrowseImage> name=NC_000913:1674364..1674404 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

</protect>

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

[back to top]


<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference


Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b1602 (EcoliWiki Page)

NCBI GEO profiles for pntB

microarray

GenExpDB:b1602 (EcoliWiki Page)

Summary of data for pntB from multiple microarray studies


Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes

<protect></protect>

Notes

Accessions Related to pntB Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG10745

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0738

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1602

EcoGene

EcoGene:EG10745

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000736

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005352

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



Evolution

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]


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

Organism Homologs (Statistics) Comments

Anopheles gambiae

  • ENSANGP00000016622 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000015392 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000003395 (score: 1.000; bootstrap: 83%)

From Inparanoid:20070104

Shigella flexneri

PNTB

From SHIGELLACYC

E. coli O157

PNTB

From ECOO157CYC


Do-It-Yourself Web Tools

<protect></protect>

Notes

Families

[back to top]


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

Database Accession Notes

Superfamily (EcoliWiki Page)

SUPERFAMILY:52467

Panther (EcoliWiki Page)

PTHR10160:SF6

Pfam (EcoliWiki Page)

PF02233 NAD(P) transhydrogenase beta subunit

EcoCyc

EcoCyc:EG10745

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10745

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000736

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0738

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005352

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



References

[back to top]


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 1.7 1.8 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 2.5 2.6 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. 3.0 3.1 3.2 3.3 3.4 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. 4.0 4.1 4.2 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 CGSC: The Coli Genetics Stock Center
  6. 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).
  7. Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed

Categories

[back to top]