phr:On One Page

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

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Standard Name

phr

Gene Synonym(s)

ECK0697, b0708, JW0698, phrB[1], phrB

Product Desc.

deoxyribodipyrimidine photolyase (photoreactivation)[2][3]

Deoxyribodipyrimidine photolyase; DNA photolyase; monomeric[4]

Product Synonyms(s)

deoxyribodipyrimidine photolyase, FAD-binding[1], B0708[2][1], Phr[2][1], PhrB[2][1] , ECK0697, JW0698, phrB, b0708

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): phr[2], phrB, ybgA-phr[2], ybgA-phrB, orf169-phr

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

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

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Notes

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The flavoprotein DNA photolyase uses light to repair cyclobutylpyrimidine dimers in DNA. The lesion is flipped out of the DNA double helix. Contains FADH2 and 5,10-MTHF chromophores.[4]



Gene

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Nomenclature

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

Standard name

phr

Mnemonic

Photoreactivation

Synonyms

ECK0697, b0708, JW0698, phrB[1], phrB

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Notes

Location(s) and DNA Sequence

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<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

15.92 minutes 

MG1655: 738730..740148
<gbrowseImage> name=NC_000913:738730..740148 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 720400..721821
<gbrowseImage> name=NC_012967:720400..721821 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 641490..642908
<gbrowseImage> name=NC_012759:641490..642908 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 739929..741347
<gbrowseImage> name=NC_007779:739929..741347 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 791322..792740
<gbrowseImage> name=NC_010473:791322..792740 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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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

738733

Edman degradation

PMID:6325460


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Notes

Alleles and Phenotypes

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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

Δphr (Keio:JW0698)

deletion

deletion

PMID:16738554

Shigen
CGSC8776[5]

phrBW278X

W278X

Reduces DNA-binding affinity

seeded from UniProt:P00914

phrBW383F

W383F

Abolishes photolyase activity

seeded from UniProt:P00914

phr-1

CGSC:4734

phr-2

CGSC:15656

Δphr-758::kan

PMID:16738554

CGSC:102368


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Notes

Genetic Interactions

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

Genetic Resources

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

Resource Resource Type Source Notes/Reference

JW0698

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACTACCCATCTGGTCTGGTT

Primer 2:CCTTTCCCCTTCCGCGCCGCCTC

3G6

Kohara Phage

Genobase

PMID:3038334

25C10S

Kohara Phage

Genobase

PMID:3038334

asnB3057::Tn10

Linked marker

CAG18433 = CGSC7349[5]

est. P1 cotransduction: 20% [6]
Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.

nadA57::Tn10

Linked marker

CAG12147 = CGSC7351[5]

est. P1 cotransduction: 18% [6]

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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

EcoCyc

EcoCyc:EG10736

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10736

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000727

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947005

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0729

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002417

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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Nomenclature

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

Standard name

Phr

Synonyms

deoxyribodipyrimidine photolyase, FAD-binding[1], B0708[2][1], Phr[2][1], PhrB[2][1] , ECK0697, JW0698, phrB, b0708

Product description

deoxyribodipyrimidine photolyase (photoreactivation)[2][3]

Deoxyribodipyrimidine photolyase; DNA photolyase; monomeric[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:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0003904

deoxyribodipyrimidine photo-lyase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:4.1.99.3

F

Seeded from EcoCyc (v14.0)

complete

GO:0003904

deoxyribodipyrimidine photo-lyase activity

PMID:6363715

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002081

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005101

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006050

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018394

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0234

P

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0227

P

Seeded from EcoCyc (v14.0)

complete

GO:0018298

protein-chromophore linkage

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0157

P

Seeded from EcoCyc (v14.0)

complete

GO:0018298

protein-chromophore linkage

PMID:2895469

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0018298

protein-chromophore linkage

PMID:6363715

IDA: Inferred from Direct Assay

P

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

nfi

PMID:15690043

Experiment(s):EBI-891771

Protein

rplQ

PMID:16606699

Experiment(s):EBI-1137743

Protein

mukB

PMID:16606699

Experiment(s):EBI-1137743

Protein

ssb

PMID:16606699

Experiment(s):EBI-1137743

Protein

rpsI

PMID:16606699

Experiment(s):EBI-1137743

Protein

rplB

PMID:16606699

Experiment(s):EBI-1137743

Protein

rplI

PMID:16606699

Experiment(s):EBI-1137743

Protein

groL

PMID:16606699

Experiment(s):EBI-1137743

Protein

rhsA

PMID:16606699

Experiment(s):EBI-1137743

Protein

nfi

PMID:19402753

LCMS(ID Probability):99.6

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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 

MTTHLVWFRQ DLRLHDNLAL AAACRNSSAR VLALYIATPR QWATHNMSPR QAELINAQLN
GLQIALAEKG IPLLFREVDD FVASVEIVKQ VCAENSVTHL FYNYQYEVNE RARDVEVERA
LRNVVCEGFD DSVILPPGAV MTGNHEMYKV FTPFKNAWLK RLREGMPECV AAPKVRSSGS
IEPSPSITLN YPRQSFDTAH FPVEEKAAIA QLRQFCQNGA GEYEQQRDFP AVEGTSRLSA
SLATGGLSPR QCLHRLLAEQ PQALDGGAGS VWLNELIWRE FYRHLITYHP SLCKHRPFIA
WTDRVQWQSN PAHLQAWQEG KTGYPIVDAA MRQLNSTGWM HNRLRMITAS FLVKDLLIDW
REGERYFMSQ LIDGDLAANN GGWQWAASTG TDAAPYFRIF NPTTQGEKFD HEGEFIRQWL
PELRDVPGKV VHEPWKWAQK AGVTLDYPQP IVEHKEARVQ TLAAYEAARK GK
Length

472

Mol. Wt

53.666 kDa

pI

7.3 (calculated)

Extinction coefficient

103,360 - 104,235 (calc based on 14 Y, 15 W, and 7 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

4..174

PF00875 DNA photolyase

PMID:19920124

Domain

203..469

PF03441 FAD binding domain of DNA photolyase

PMID:19920124

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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=phr 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:16128683

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947005

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002417

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P00914

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10736

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10736

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947005

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000727

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0729

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Expression

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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

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See Help:Cellular levels

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

Protein

Ecoli K-12

3.476+/-0.049

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

Protein

E. coli K-12 MG1655

21

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

37

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

5a

molecules/cell/generation

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

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation

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<protect>

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

Transcription unit(s)

phr

ybgA-phr

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Figure courtesy of RegulonDB

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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

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<protect><gbrowseImage> name=NC_000913:738710..738750 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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

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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

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

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b0708 (EcoliWiki Page)

NCBI GEO profiles for phr

microarray

GenExpDB:b0708 (EcoliWiki Page)

Summary of data for phr from multiple microarray studies

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

Resource Name Resource Type Description Source Notes
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Notes

Accessions Related to phr Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10736

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0729

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0708

EcoGene

EcoGene:EG10736

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000727

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002417

Escherichia coli str. K-12 substr. MG1655

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Notes

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Evolution

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Homologs in Other Organisms

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

Organism Homologs (Statistics) Comments

Anopheles gambiae

  • ENSANGP00000013343 (score: 1.000; bootstrap: 100%)
  • ENSANGP00000013228 (score: 0.369)
  • ENSANGP00000019076 (score: 0.176)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT4G08920 (score: 1.000; bootstrap: 84%)
  • AT1G04400 (score: 0.370)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000028277 (score: 1.000; bootstrap: 100%)
  • ENSBTAP00000037877 (score: 0.527)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000013814 (score: 1.000; bootstrap: 100%)
  • ENSCAFP00000002620 (score: 0.706)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-040617-2 (score: 1.000; bootstrap: 59%)
  • ZDB-CDNA-050706-5 (score: 1.000; bootstrap: 59%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0016054 (score: 1.000; bootstrap: 100%)
  • FBgn0025680 (score: 0.180)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA15376-PA (score: 1.000; bootstrap: 100%)
  • GA17677-PA (score: 0.190)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000000142 (score: 1.000; bootstrap: 100%)
  • ENSGALP00000020598 (score: 0.420)
  • ENSGALP00000013730 (score: 0.347)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000263762 (score: 1.000; bootstrap: 100%)
  • ENSP00000008527 (score: 0.686)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000003303 (score: 1.000; bootstrap: 100%)
  • ENSMMUP00000028723 (score: 0.688)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000024807 (score: 1.000; bootstrap: 100%)
  • ENSMODP00000001926 (score: 0.611)

From Inparanoid:20070104

Mus musculus

  • MGI:1270859 (score: 1.000; bootstrap: 100%)
  • MGI:1270841 (score: 0.687)

From Inparanoid:20070104

Oryza gramene

  • Q5MD22 (score: 1.000; bootstrap: 88%)
  • Q8H6B3 (score: 0.989)
  • Q948J4 (score: 0.850)
  • Q7XV36 (score: 0.849)
  • Q948J6 (score: 0.755)
  • Q6YXC2 (score: 0.755)
  • Q7XXN9 (score: 0.658)
  • Q9SXI0 (score: 0.426)
  • Q712D5 (score: 0.334)
  • Q852P4 (score: 0.333)
  • Q70YK6 (score: 0.331)
  • Q712D6 (score: 0.150)
  • Q6K1S1 (score: 0.079)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000006139 (score: 1.000; bootstrap: 100%)
  • ENSPTRP00000009157 (score: 0.604)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000010142 (score: 1.000; bootstrap: 100%)
  • ENSRNOP00000033441 (score: 0.681)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YOR386W (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000129951 (score: 1.000; bootstrap: 65%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00021451001 (score: 1.000; bootstrap: 94%)
  • GSTENP00023788001 (score: 0.127)
  • GSTENP00021379001 (score: 0.103)
  • GSTENP00008509001 (score: 0.096)
  • GSTENP00008508001 (score: 0.085)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000008500 (score: 1.000; bootstrap: 56%)
  • ENSXETP00000036934 (score: 0.507)
  • ENSXETP00000033570 (score: 0.395)
  • ENSXETP00000002230 (score: 0.374)

From Inparanoid:20070104

Shigella flexneri

PHRB

From SHIGELLACYC

E. coli O157

PHRB

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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

Database Accession Notes

Pfam (EcoliWiki Page)

PF03441 FAD binding domain of DNA photolyase

Pfam (EcoliWiki Page)

PF00875 DNA photolyase

Superfamily (EcoliWiki Page)

SUPERFAMILY:48173

Superfamily (EcoliWiki Page)

SUPERFAMILY:52425

Panther (EcoliWiki Page)

PTHR11455:SF0

EcoCyc

EcoCyc:EG10736

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10736

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000727

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0729

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002417

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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 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 2.9 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. ↑ 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).

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