rfaD: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

RfaD

Synonyms

ADP-L-glycero-D-mannoheptose-6-epimerase, NAD(P)-binding[1], B3619[2][1], HldD[2][1], WaaD[2][1], NbsB[2][1], HtrM[2][1], RfaD[2][1] , ECK3609, gmhD, hldD, htrM, JW3594, waaD, b3619

Product description

ADP-L-glycero-D-mannoheptose-6-epimerase[2][3];

Component of ADP-L-glycero-D-mannoheptose-6-epimerase[3]

ADP-L-glycero-D-manno-heptose-6-epimerase; heat-inducible, LPS; allows high-temperature growth[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:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0009435

NAD biosynthetic process

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001509

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016040

F

Seeded from EcoCyc (v14.0)

complete

GO:0005829

cytosol

PMID:16858726[5]

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01601

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011912

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0119

P

Seeded from EcoCyc (v14.0)

complete

GO:0006950

response to stress

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0346

P

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016040

P

Seeded from EcoCyc (v14.0)

complete

GO:0008712

ADP-glyceromanno-heptose 6-epimerase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01601

F

Seeded from EcoCyc (v14.0)

complete

GO:0008712

ADP-glyceromanno-heptose 6-epimerase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011912

F

Seeded from EcoCyc (v14.0)

complete

GO:0008712

ADP-glyceromanno-heptose 6-epimerase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:5.1.3.20

F

Seeded from EcoCyc (v14.0)

complete

GO:0009103

lipopolysaccharide biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0448

P

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

PMID:16858726[5]

IDA: Inferred from Direct Assay

C

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:0044237

cellular metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001509

P

Seeded from EcoCyc (v14.0)

complete

GO:0050661

NADP or NADPH binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011912

F

Seeded from EcoCyc (v14.0)

complete

GO:0050662

coenzyme binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001509

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 ADP-L-glycero-D-mannoheptose-6-epimerase

could be indirect

Protein

groL

PMID:16606699[6]

Experiment(s):EBI-1146271

Protein

cysM

PMID:15690043[7]

Experiment(s):EBI-884306

Protein

dnaK

PMID:15690043[7]

Experiment(s):EBI-884306

Protein

entF

PMID:15690043[7]

Experiment(s):EBI-884306

Protein

rplO

PMID:15690043[7]

Experiment(s):EBI-884306

Protein

rpsG

PMID:15690043[7]

Experiment(s):EBI-884306, EBI-891254

Protein

ybjX

PMID:15690043[7]

Experiment(s):EBI-884306, EBI-879208

Protein

ddpD

PMID:15690043[7]

Experiment(s):EBI-891254

Protein

rplC

PMID:15690043[7]

Experiment(s):EBI-891254

Protein

rplS

PMID:15690043[7]

Experiment(s):EBI-891254

Protein

secA

PMID:15690043[7]

Experiment(s):EBI-891254

Protein

torA

PMID:15690043[7]

Experiment(s):EBI-891254

Protein

ydaY

PMID:15690043[7]

Experiment(s):EBI-891254

Protein

yhhN

PMID:15690043[7]

Experiment(s):EBI-891254

Protein

yhjS

PMID:15690043[7]

Experiment(s):EBI-891254

Protein

rplS

PMID:19402753[8]

LCMS(ID Probability):99.0 MALDI(Z-score):23.522411

Protein

torA

PMID:19402753[8]

LCMS(ID Probability):99.0

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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

Cytoplasm

PMID:2198271[9]

EchoLocation:rfaD


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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 

MIIVTGGAGF IGSNIVKALN DKGITDILVV DNLKDGTKFV NLVDLNIADY MDKEDFLIQI
MAGEEFGDVE AIFHEGACSS TTEWDGKYMM DNNYQYSKEL LHYCLEREIP FLYASSAATY
GGRTSDFIES REYEKPLNVY GYSKFLFDEY VRQILPEANS QIVGFRYFNV YGPREGHKGS
MASVAFHLNT QLNNGESPKL FEGSENFKRD FVYVGDVADV NLWFLENGVS GIFNLGTGRA
ESFQAVADAT LAYHKKGQIE YIPFPDKLKG RYQAFTQADL TNLRAAGYDK PFKTVAEGVT
EYMAWLNRDA
Length

310

Mol. Wt

34.893 kDa

pI

4.7 (calculated)

Extinction coefficient

44,810 - 45,060 (calc based on 19 Y, 3 W, and 2 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

2..236

PF01370 NAD dependent epimerase/dehydratase family

PMID:19920124[10]

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

Structures

<beststructure> gene=rfaD 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:16131490

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948134

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011843

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P67910

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10838

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10838

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948134

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000829

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0831

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 1.7 1.8 1.9 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 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. ↑ 5.0 5.1 Lasserre, JP et al. (2006) A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis. Electrophoresis 27 3306-21 PubMed
  6. ↑ 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 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  8. ↑ 8.0 8.1 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  9. ↑ Pegues, JC et al. (1990) Cloning, expression, and characterization of the Escherichia coli K-12 rfaD gene. J. Bacteriol. 172 4652-60 PubMed
  10. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

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