deoB: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

deoB

Gene Synonym(s)

ECK4375, b4383, JW4346, drm, thyR, tlr[1], tlr

Product Desc.

PPENTOMUT- Phosphopentomutase; deoxyribouratase[2]

Product Synonyms(s)

phosphopentomutase [1], B4383 [3][1], Tlr [3][1], Drm [3][1], ThyR [3][1], DeoB [3][1] , drm, ECK4375, JW4346, thyR, tlr, b4383

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): deoBD[3], deoCABD[3], OP00024, deo

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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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

deoB

Mnemonic

Deoxyribose

Synonyms

ECK4375, b4383, JW4346, drm, thyR, tlr[1], tlr

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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

99.52 minutes, 99.52 minutes 

MG1655: 4617626..4618849
<gbrowseImage> name=NC_000913:4617626..4618849 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4608837..4610060
<gbrowseImage> name=NC_012967:4608837..4610060 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4556110..4557333
<gbrowseImage> name=NC_012759:4556110..4557333 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4624283..4625506
<gbrowseImage> name=NC_007779:4624283..4625506 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4664088..4665311
<gbrowseImage> name=NC_010473:4664088..4665311 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

4617626

Edman degradation

PMID:6087276


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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

ΔdeoB (Keio:JW4346)

deletion

deletion

PMID:16738554

Shigen
CGSC11101[4]

ΔdeoB::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938

ΔdeoB::kan

deletion

Biolog:respiration

unable to respire Inosine

PMID:16095938

ΔdeoB::kan

deletion

Biolog:respiration

unable to respire Uridine

PMID:16095938

deoB16

CGSC:5324

deoB20

CGSC:7050

deoB37

CGSC:7272

deoB13

CGSC:8313

deoB301

CGSC:8418

deoB11

CGSC:9233

deoB12

CGSC:9247

deoB23

CGSC:10131

deoB14

CGSC:10171

deoB17

CGSC:14624

deoB7

CGSC:16359

deoB9

CGSC:16361

deoB15

CGSC:17077

deoB998

CGSC:39229

deoB6

CGSC:72572

ΔdeoB779::kan

PMID:16738554

CGSC:100576


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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

JW4346

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAACGTGCATTTATTATGGT

Primer 2:CCGAACATGGCTTTGCCATATTC

15C9

Kohara Phage

Genobase

PMID:3038334

mdoB202::Tn10

Linked marker

CAG18430 = CGSC7488[4]

est. P1 cotransduction: 40% [5]
Synonyms:zjj-202::Tn10, zji-202::Tn10

thrA34::Tn10

Linked marker

CAG18442 = CGSC7320[4]

est. P1 cotransduction: 44% [5]
Synonyms:thr-34::Tn10

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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:EG10220

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10220

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000214

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948910

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0216

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014377

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

DeoB

Synonyms

phosphopentomutase [1], B4383 [3][1], Tlr [3][1], Drm [3][1], ThyR [3][1], DeoB [3][1] , drm, ECK4375, JW4346, thyR, tlr, b4383

Product description

PPENTOMUT- Phosphopentomutase; deoxyribouratase[2]

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:0000287

magnesium ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010045

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006124

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017850

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00740

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010045

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017850

P

Seeded from EcoCyc (v14.0)

complete

GO:0008973

phosphopentomutase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00740

F

Seeded from EcoCyc (v14.0)

complete

GO:0008973

phosphopentomutase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010045

F

Seeded from EcoCyc (v14.0)

complete

GO:0008973

phosphopentomutase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:5.4.2.7

F

Seeded from EcoCyc (v14.0)

complete

GO:0009117

nucleotide metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010045

P

Seeded from EcoCyc (v14.0)

complete

GO:0009264

deoxyribonucleotide catabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00740

P

Seeded from EcoCyc (v14.0)

complete

GO:0016853

isomerase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0413

F

Seeded from EcoCyc (v14.0)

complete

GO:0030145

manganese ion binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00740

F

Seeded from EcoCyc (v14.0)

complete

GO:0030145

manganese ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0464

F

Seeded from EcoCyc (v14.0)

complete

GO:0043094

cellular metabolic compound salvage

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010045

P

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006124

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

GO:0006974

response to DNA damage stimulus

PMID:11967071

IEP: Inferred from Expression Pattern

P

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

rseB

PMID:16606699

Experiment(s):EBI-1147952

Protein

yliI

PMID:16606699

Experiment(s):EBI-1147952

Protein

rplS

PMID:16606699

Experiment(s):EBI-1147952

Protein

intE

PMID:16606699

Experiment(s):EBI-1147952
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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 

MKRAFIMVLD SFGIGATEDA ERFGDVGADT LGHIAEACAK GEADNGRKGP LNLPNLTRLG
LAKAHEGSTG FIPAGMDGNA EVIGAYAWAH EMSSGKDTPS GHWEIAGVPV LFEWGYFSDH
ENSFPQELLD KLVERANLPG YLGNCHSSGT VILDQLGEEH MKTGKPIFYT SADSVFQIAC
HEETFGLDKL YELCEIAREE LTNGGYNIGR VIARPFIGDK AGNFQRTGNR HDLAVEPPAP
TVLQKLVDEK HGQVVSVGKI ADIYANCGIT KKVKATGLDA LFDATIKEMK EAGDNTIVFT
NFVDFDSSWG HRRDVAGYAA GLELFDRRLP ELMSLLRDDD ILILTADHGC DPTWTGTDHT
REHIPVLVYG PKVKPGSLGH RETFADIGQT LAKYFGTSDM EYGKAMF
Length

407

Mol. Wt

44.37 kDa

pI

5.1 (calculated)

Extinction coefficient

43,890 - 44,640 (calc based on 11 Y, 5 W, and 6 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

Modification Site

100

phosphorylation site at S100

probability greater than 75%

PMID:17938405

Modification Site

98

phosphorylation site at T98

probability less than 75%

PMID:17938405

Domain

2..406

PF01676 Metalloenzyme superfamily

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=deoB 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:16132200

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948910

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014377

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A6K6

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10220

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10220

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948910

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000214

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0216

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

E. coli K-12 MC4100

3.09E+03

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

Ecoli K-12

186.799+/-1.25

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.32962+/-0.10931

Molecules/cell

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

by FISH

PMID:20671182

mRNA

Ecoli K-12

0.150040883

Molecules/cell

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

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

2087

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

1012

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

1501

molecules/cell/generation

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

Ribosome Profiling

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)

deoBD

deoCABD

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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_000913:4617606..4617646 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:b4383 (EcoliWiki Page)

NCBI GEO profiles for deoB

microarray

GenExpDB:b4383 (EcoliWiki Page)

Summary of data for deoB 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

GFP Fusion

Intergenic region (4617044..4617192) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ05; Well:B4[6]

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Notes

Accessions Related to deoB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10220

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0216

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4383

EcoGene

EcoGene:EG10220

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000214

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014377

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

Shigella flexneri

DEOB

From SHIGELLACYC

E. coli O157

DEOB

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)

PF01676 Metalloenzyme superfamily

Superfamily (EcoliWiki Page)

SUPERFAMILY:53649

Panther (EcoliWiki Page)

PTHR21110:SF0

Superfamily (EcoliWiki Page)

SUPERFAMILY:143856

EcoCyc

EcoCyc:EG10220

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10220

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000214

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0216

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014377

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 1.11 1.12 1.13 1.14 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  3. ↑ 3.00 3.01 3.02 3.03 3.04 3.05 3.06 3.07 3.08 3.09 3.10 3.11 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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).
  6. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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