rhmA:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

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Standard name

RhmA

Synonyms

predicted 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase[1], B2245[2][1], RhmA[2][1] , ECK2238, JW2239, yfaU, b2245

Product description

predicted aldolase[2][3]. Crystal structure shows that RhmA is a metal-dependent class II aldolase belonging to the pyruvate/enolpyruvate binding (�/R)8 barrel superfamily.[4], Genomic context suggested a 2-dehydro-3-deoxy sugar aldolase function rather than the 4-hydroxy-2-ketoheptane- 1,7-dioate aldolase function as annotated in the databases based on homology with the related HpcH. Functional assignment of YfaW as a L-rhamnonate dehydratase suggested 2-dehydro-3-deoxy-L-rhamnonate is the physiological substrate of RhmA, and enzyme kinetic measurements support this assignment.

Putative HHED aldolase, function unknown[5]

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:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

F

Seeded from EcoCyc (v14.0)

complete

GO:0005515

protein binding

PMID:18754683[4]

IPI: Inferred from Physical Interaction

F

Seeded from EcoCyc (v14.0)

Missing: with/from

GO:0006725

cellular aromatic compound metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005000

P

Seeded from EcoCyc (v14.0)

complete

GO:0016151

nickel ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0533

F

Seeded from EcoCyc (v14.0)

complete

GO:0016832

aldehyde-lyase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01290

F

Seeded from EcoCyc (v14.0)

complete

GO:0016832

aldehyde-lyase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:4.1.2

F

Seeded from EcoCyc (v14.0)

complete

GO:0000287

magnesium ion binding

PMID:18754683[4]

IPI: Inferred from Physical Interaction

F

Missing: with/from

GO:0006725

cellular aromatic compound metabolic process

PMID:18754683[4]

ISS: Inferred from Sequence or Structural Similarity

UniProtKB:Q47098

P

complete

GO:0016151

nickel ion binding

PMID:18754683[4]

IDA: Inferred from Direct Assay

F

complete

GO:0016832

aldehyde-lyase activity

PMID:18754683[4]

IDA: Inferred from Direct Assay

F

complete

GO:0005737

cytoplasm

PMID:18754683[4]

IDA: Inferred from Direct Assay

C

complete

GO:0005515

protein binding

PMID:18754683[4]

IPI: Inferred from Physical Interaction

EcoliWiki:yfaU

F

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
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Notes

Localization

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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 

MNALLSNPFK ERLRKGEVQI GLWLSSTTAY MAEIAATSGY DWLLIDGEHA PNTIQDLYHQ
LQAVAPYASQ PVIRPVEGSK PLIKQVLDIG AQTLLIPMVD TAEQARQVVS ATRYPPYGER
GVGASVARAA RWGRIENYMA QVNDSLCLLV QVESKTALDN LDEILDVEGI DGVFIGPADL
SASLGYPDNA GHPEVQRIIE TSIRRIRAAG KAAGFLAVAP DMAQQCLAWG ANFVAVGVDT
MLYSDALDQR LAMFKSGKNG PRIKGSY
Length

267

Mol. Wt

28.916 kDa

pI

5.2 (calculated)

Extinction coefficient

36,900 - 37,150 (calc based on 10 Y, 4 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

19..246

PF03328 HpcH/HpaI aldolase/citrate lyase family

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=yfaU 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:16130180

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948054

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007431

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P76469

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7158

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14083

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948054

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003734

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3836

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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 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. ↑ 4.0 4.1 4.2 4.3 4.4 4.5 4.6 4.7 Rea, D et al. (2008) Crystal structure and functional assignment of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12. Biochemistry 47 9955-65 PubMed
  5. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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