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P23522 (GARL_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 118. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
5-keto-4-deoxy-D-glucarate aldolase

Short name=KDGluc aldolase
Short name=KDGlucA
EC=4.1.2.20
Alternative name(s):
2-dehydro-3-deoxy-D-glucarate aldolase
2-keto-3-deoxy-D-glucarate aldolase
5-dehydro-4-deoxy-D-glucarate aldolase
Alpha-keto-beta-deoxy-D-glucarate aldolase
Gene names
Name:garL
Synonyms:yhaF
Ordered Locus Names:b3126, JW3095
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length256 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the reversible retro-aldol cleavage of both 5-keto-4-deoxy-D-glucarate and 2-keto-3-deoxy-D-glucarate to pyruvate and tartronic semialdehyde. Ref.4 Ref.5

Catalytic activity

5-dehydro-4-deoxy-D-glucarate = pyruvate + tartronate semialdehyde. Ref.4

2-dehydro-3-deoxy-D-glucarate = pyruvate + tartronate semialdehyde. Ref.4

Cofactor

Binds 1 magnesium ion per subunit. Can also use, although less efficiently, Co2+, Fe2+ and Mn2+. Ref.5

Enzyme regulation

Inhibited by acetate, chloride and bromide ions, nitrate, fluoride, cyanide, EDTA and pyrophosphate. Ref.5

Pathway

Carbohydrate acid metabolism; D-galactarate degradation; D-glycerate from D-galactarate: step 2/3. HAMAP-Rule MF_01291

Subunit structure

Homohexamer; trimer of dimers. Ref.7

Miscellaneous

The catalytic mechanism was originally (Ref.7) thought to use a phosphate as the catalytic acid, but this was subsequently disputed (PubMed:15996099, PubMed:17881002 and PubMed:18754683).

Sequence similarities

Belongs to the HpcH/HpaI aldolase family. KDGluc aldolase subfamily.

Caution

Was wrongly named 2-dehydro-3-deoxygalactarate aldolase (DDG aldolase or DDGA) in Ref.7. 2-dehydro-3-deoxygalactarate is the enantiomer of 5-dehydro-4-deoxy-D-glucarate, but is not an isomer obtained in the degradation pathway of D-glucarate/galactarate and the enzyme has not been shown to be active on it.

Biophysicochemical properties

Kinetic parameters:

KM=65 µM for 5-keto-4-deoxy-D-glucarate Ref.4

pH dependence:

Optimum pH is 7.4-8.6. Stable from pH 6 to 7.5.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 2562565-keto-4-deoxy-D-glucarate aldolase HAMAP-Rule MF_01291
PRO_0000207093

Sites

Active site501Proton acceptor By similarity
Metal binding1531Magnesium
Metal binding1791Magnesium
Binding site1511Substrate
Binding site1781Substrate; via amide nitrogen
Binding site1791Substrate
Site751Transition state stabilizer By similarity
Site891Increases basicity of active site His By similarity

Secondary structure

................................................. 256
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P23522 [UniParc].

Last modified November 1, 1995. Version 2.
Checksum: 8E6345EE3F1CFCDB

FASTA25627,384
        10         20         30         40         50         60 
MNNDVFPNKF KAALAAKQVQ IGCWSALSNP ISTEVLGLAG FDWLVLDGEH APNDISTFIP 

        70         80         90        100        110        120 
QLMALKGSAS APVVRVPTNE PVIIKRLLDI GFYNFLIPFV ETKEEAELAV ASTRYPPEGI 

       130        140        150        160        170        180 
RGVSVSHRAN MFGTVADYFA QSNKNITILV QIESQQGVDN VDAIAATEGV DGIFVGPSDL 

       190        200        210        220        230        240 
AAALGHLGNA SHPDVQKAIQ HIFNRASAHG KPSGILAPVE ADARRYLEWG ATFVAVGSDL 

       250 
GVFRSATQKL ADTFKK 

« Hide

References

« Hide 'large scale' references
[1]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[2]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]"Precise mapping of the rnpB gene encoding the RNA component of RNase P in Escherichia coli K-12."
Komine Y., Inokuchi H.
J. Bacteriol. 173:1813-1816(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 89-256.
Strain: K12.
[4]"Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli."
Hubbard B.K., Koch M., Palmer D.R., Babbitt P.C., Gerlt J.A.
Biochemistry 37:14369-14375(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 1-16, FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS.
Strain: K12 / MG1655 / ATCC 47076.
[5]"2-keto-3-deoxy-D-glucarate aldolase."
Fish D.C., Blumenthal H.J.
Methods Enzymol. 9:529-534(1966)
Cited for: FUNCTION, CHARACTERIZATION, SUBSTRATE SPECIFICITY, COFACTOR, ENZYME REGULATION, PH DEPENDENCE.
Strain: K12 / CR63.
[6]"A common regulator for the operons encoding the enzymes involved in D-galactarate, D-glucarate, and D-glycerate utilization in Escherichia coli."
Monterrubio R., Baldoma L., Obradors N., Aguilar J., Badia J.
J. Bacteriol. 182:2672-2674(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: GENE NAME.
[7]"Crystal structures of the metal-dependent 2-dehydro-3-deoxy-galactarate aldolase suggest a novel reaction mechanism."
Izard T., Blackwell N.C.
EMBO J. 19:3849-3856(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEXES WITH MAGNESIUM AND PYRUVATE, SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U18997 Genomic DNA. Translation: AAA57929.1.
U00096 Genomic DNA. Translation: AAC76160.1.
AP009048 Genomic DNA. Translation: BAE77173.1.
D90212 Genomic DNA. Translation: BAA14237.1.
PIRB65102.
RefSeqNP_417595.1. NC_000913.3.
YP_491314.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1DXEX-ray1.80A/B1-256[»]
1DXFX-ray2.60A/B1-256[»]
ProteinModelPortalP23522.
SMRP23522. Positions 4-256.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-9740N.
IntActP23522. 9 interactions.
STRING511145.b3126.

PTM databases

PhosSiteP0809389.

Proteomic databases

PaxDbP23522.
PRIDEP23522.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76160; AAC76160; b3126.
BAE77173; BAE77173; BAE77173.
GeneID12930493.
947630.
KEGGecj:Y75_p3048.
eco:b3126.
PATRIC32121666. VBIEscCol129921_3219.

Organism-specific databases

EchoBASEEB0016.
EcoGeneEG10016. garL.

Phylogenomic databases

eggNOGCOG3836.
HOGENOMHOG000179750.
KOK01630.
OMAHAPNDIT.
OrthoDBEOG6NPM5P.
PhylomeDBP23522.
ProtClustDBPRK10558.

Enzyme and pathway databases

BioCycEcoCyc:KDGALDOL-MONOMER.
ECOL316407:JW3095-MONOMER.
MetaCyc:KDGALDOL-MONOMER.
UniPathwayUPA00565; UER00630.

Gene expression databases

GenevestigatorP23522.

Family and domain databases

Gene3D3.20.20.60. 1 hit.
HAMAPMF_01291. KDGluc_aldolase.
InterProIPR005000. Aldehyde-lyase_domain.
IPR017648. Dehyd-dGlucarate-aldolase_GarL.
IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
[Graphical view]
PfamPF03328. HpcH_HpaI. 1 hit.
[Graphical view]
SUPFAMSSF51621. SSF51621. 1 hit.
TIGRFAMsTIGR03239. GarL. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP23522.
PROP23522.

Entry information

Entry nameGARL_ECOLI
AccessionPrimary (citable) accession number: P23522
Secondary accession number(s): Q2M983
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1991
Last sequence update: November 1, 1995
Last modified: April 16, 2014
This is version 118 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene