rutA: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

YcdM

Synonyms

predicted monooxygenase[1], YcdM[2][1], B1012[2][1], RutA[2][1] , ECK1003, JW0997, ycdM, b1012

Product description

predicted coenzyme F420-dependent N5,N10-methylenetetrahydromethanopterin reductase[2][3]

Gene in rut operon for pyrimidine nitrogen catabolism; putative luciferase-like monooxygenase[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:0004497

monooxygenase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0503

F

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: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

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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

ompL

PMID:16606699[5]

Experiment(s):EBI-1138614

Protein

yodC

PMID:16606699[5]

Experiment(s):EBI-1138614

Protein

ymfG

PMID:16606699[5]

Experiment(s):EBI-1138614

Protein

dnaK

PMID:16606699[5]

Experiment(s):EBI-1138614

Protein

yghW

PMID:16606699[5]

Experiment(s):EBI-1138614

Protein

nadE

PMID:16606699[5]

Experiment(s):EBI-1138614

Protein

rplB

PMID:16606699[5]

Experiment(s):EBI-1138614
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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 

MQDAAPRLTF TLRDEERLMM KIGVFVPIGN NGWLISTHAP QYMPTFELNK AIVQKAEHYH
FDFALSMIKL RGFGGKTEFW DHNLESFTLM AGLAAVTSRI QIYATAATLT LPPAIVARMA
ATIDSISGGR FGVNLVTGWQ KPEYEQMGIW PGDDYFSRRY DYLTEYVQVL RDLWGTGKSD
FKGDFFTMND CRVSPQPSVP MKVICAGQSD AGMAFSARYA DFNFCFGKGV NTPTAFAPTA
ARMKQAAEQT GRDVGSYVLF MVIADETDDA ARAKWEHYKA GADEEALSWL TEQSQKDTRS
GTDTNVRQMA DPTSAVNINM GTLVGSYASV ARMLDEVASV PGAEGVLLTF DDFLSGIETF
GERIQPLMQC RAHLPALTQE VA
Length

382

Mol. Wt

42.219 kDa

pI

5.0 (calculated)

Extinction coefficient

56,380 - 56,880 (calc based on 12 Y, 7 W, and 4 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

20..344

PF00296 Luciferase-like monooxygenase

PMID:19920124[6]

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

Structures

<beststructure> gene=rutA 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:49176071

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945643

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003416

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P75898

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6523

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13859

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945643

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003123

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3619

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 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 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 5.2 5.3 5.4 5.5 5.6 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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