garL: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

GarL

Synonyms

alpha-dehydro-beta-deoxy-D-glucarate aldolase[1], B3126[2][1], YhaF[2][1], GarL[2][1] , ECK3114, JW3095, yhaF, b3126

Product description

2-dehydro-3-deoxygalactarate aldolase; homohexameric[3]

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: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:0005506

iron ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0408

F

Seeded from EcoCyc (v14.0)

complete

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:0008672

2-dehydro-3-deoxyglucarate aldolase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01291

F

Seeded from EcoCyc (v14.0)

complete

GO:0008672

2-dehydro-3-deoxyglucarate aldolase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:4.1.2.20

F

Seeded from EcoCyc (v14.0)

complete

GO:0019582

D-galactarate catabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01291

P

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: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:0050897

cobalt ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0170

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

PMID:9772162[4]

IDA: Inferred from Direct Assay

C

complete

GO:0019394

glucarate catabolic process

PMID:9772162[4]

IDA: Inferred from Direct Assay

P

complete

GO:0008672

2-dehydro-3-deoxyglucarate aldolase activity

PMID:9772162[4]

IDA: Inferred from Direct Assay

F

complete

GO:0016830

carbon-carbon lyase activity

PMID:9772162[4]

IDA: Inferred from Direct Assay

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

Protein

uvrY

PMID:16606699[5]

Experiment(s):EBI-1144847

Protein

mfd

PMID:16606699[5]

Experiment(s):EBI-1144847

Protein

mngB

PMID:16606699[5]

Experiment(s):EBI-1144847

Protein

lacZ

PMID:16606699[5]

Experiment(s):EBI-1144847

Protein

nadE

PMID:16606699[5]

Experiment(s):EBI-1144847

Protein

yebT

PMID:16606699[5]

Experiment(s):EBI-1144847

Protein

modB

PMID:16606699[5]

Experiment(s):EBI-1144847
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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 

MNNDVFPNKF KAALAAKQVQ IGCWSALSNP ISTEVLGLAG FDWLVLDGEH APNDISTFIP
QLMALKGSAS APVVRVPTNE PVIIKRLLDI GFYNFLIPFV ETKEEAELAV ASTRYPPEGI
RGVSVSHRAN MFGTVADYFA QSNKNITILV QIESQQGVDN VDAIAATEGV DGIFVGPSDL
AAALGHLGNA SHPDVQKAIQ HIFNRASAHG KPSGILAPVE ADARRYLEWG ATFVAVGSDL
GVFRSATQKL ADTFKK
Length

256

Mol. Wt

27.383 kDa

pI

6.0 (calculated)

Extinction coefficient

22,460 - 22,585 (calc based on 4 Y, 3 W, and 1 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

124

phosphorylation site at S124

probability greater than 75%

PMID:17938405[6]

Domain

20..246

PF03328 HpcH/HpaI aldolase/citrate lyase family

PMID:19920124[7]

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

Structures

<beststructure> gene=garL 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:16131018

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947630

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010276

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P23522

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10016

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10016

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947630

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000014

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0016

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 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. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  4. ↑ 4.0 4.1 4.2 4.3 Hubbard, BK et al. (1998) Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli. Biochemistry 37 14369-75 PubMed
  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. ↑ Macek, B et al. (2008) Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation. Mol. Cell Proteomics 7 299-307 PubMed
  7. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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