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Protein

5-keto-4-deoxy-D-glucarate aldolase

Gene

garL

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.2 Publications

Catalytic activityi

5-dehydro-4-deoxy-D-glucarate = pyruvate + tartronate semialdehyde.1 Publication
2-dehydro-3-deoxy-D-glucarate = pyruvate + tartronate semialdehyde.1 Publication

Cofactori

Mg2+1 Publication, Co2+1 Publication, Fe2+1 Publication, Mn2+1 PublicationNote: Binds 1 Mg(2+) ion per subunit. Can also use, although less efficiently, Co(2+), Fe(2+) and Mn2+.1 Publication

Enzyme regulationi

Inhibited by acetate, chloride and bromide ions, nitrate, fluoride, cyanide, EDTA and pyrophosphate.1 Publication

Kineticsi

  1. KM=65 µM for 5-keto-4-deoxy-D-glucarate1 Publication

pH dependencei

Optimum pH is 7.4-8.6. Stable from pH 6 to 7.5.1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei50 – 501Proton acceptorBy similarity
Sitei75 – 751Transition state stabilizerBy similarity
Sitei89 – 891Increases basicity of active site HisBy similarity
Binding sitei151 – 1511Substrate
Metal bindingi153 – 1531Magnesium
Binding sitei178 – 1781Substrate; via amide nitrogen
Metal bindingi179 – 1791Magnesium
Binding sitei179 – 1791Substrate

GO - Molecular functioni

  1. 2-dehydro-3-deoxyglucarate aldolase activity Source: EcoliWiki
  2. carbon-carbon lyase activity Source: EcoliWiki
  3. magnesium ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. D-glucarate catabolic process Source: EcoCyc
  2. galactarate catabolic process Source: EcoCyc
  3. glucarate catabolic process Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Cobalt, Iron, Magnesium, Manganese, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:KDGALDOL-MONOMER.
ECOL316407:JW3095-MONOMER.
MetaCyc:KDGALDOL-MONOMER.
BRENDAi4.1.2.20. 2026.
UniPathwayiUPA00565; UER00630.

Names & Taxonomyi

Protein namesi
Recommended name:
5-keto-4-deoxy-D-glucarate aldolase (EC:4.1.2.20)
Short name:
KDGluc aldolase
Short name:
KDGlucA
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 namesi
Name:garL
Synonyms:yhaF
Ordered Locus Names:b3126, JW3095
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10016. garL.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: EcoliWiki
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 2562565-keto-4-deoxy-D-glucarate aldolasePRO_0000207093Add
BLAST

Proteomic databases

PaxDbiP23522.
PRIDEiP23522.

Expressioni

Gene expression databases

GenevestigatoriP23522.

Interactioni

Subunit structurei

Homohexamer; trimer of dimers.1 Publication

Protein-protein interaction databases

DIPiDIP-9740N.
IntActiP23522. 9 interactions.
STRINGi511145.b3126.

Structurei

Secondary structure

1
256
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi9 – 157Combined sources
Beta strandi20 – 256Combined sources
Helixi30 – 367Combined sources
Beta strandi42 – 5211Combined sources
Helixi55 – 6410Combined sources
Turni65 – 673Combined sources
Beta strandi69 – 757Combined sources
Beta strandi77 – 793Combined sources
Helixi81 – 899Combined sources
Beta strandi94 – 985Combined sources
Helixi103 – 1119Combined sources
Turni116 – 1183Combined sources
Beta strandi125 – 1273Combined sources
Helixi128 – 1303Combined sources
Turni131 – 1344Combined sources
Helixi138 – 1425Combined sources
Beta strandi147 – 1526Combined sources
Helixi155 – 1595Combined sources
Helixi161 – 1655Combined sources
Beta strandi172 – 1754Combined sources
Helixi177 – 1837Combined sources
Helixi193 – 20816Combined sources
Beta strandi213 – 2164Combined sources
Helixi220 – 2289Combined sources
Beta strandi233 – 2386Combined sources
Helixi239 – 25416Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DXEX-ray1.80A/B1-256[»]
1DXFX-ray2.60A/B1-256[»]
ProteinModelPortaliP23522.
SMRiP23522. Positions 4-256.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP23522.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG3836.
HOGENOMiHOG000179750.
InParanoidiP23522.
KOiK01630.
OMAiVRPPCNE.
OrthoDBiEOG6NPM5P.
PhylomeDBiP23522.

Family and domain databases

Gene3Di3.20.20.60. 1 hit.
HAMAPiMF_01291. KDGluc_aldolase.
InterProiIPR005000. Aldolase/citrate-lyase_domain.
IPR017648. Dehyd-dGlucarate-aldolase_GarL.
IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
[Graphical view]
PfamiPF03328. HpcH_HpaI. 1 hit.
[Graphical view]
SUPFAMiSSF51621. SSF51621. 1 hit.
TIGRFAMsiTIGR03239. GarL. 1 hit.

Sequencei

Sequence statusi: Complete.

P23522-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNNDVFPNKF KAALAAKQVQ IGCWSALSNP ISTEVLGLAG FDWLVLDGEH
60 70 80 90 100
APNDISTFIP QLMALKGSAS APVVRVPTNE PVIIKRLLDI GFYNFLIPFV
110 120 130 140 150
ETKEEAELAV ASTRYPPEGI RGVSVSHRAN MFGTVADYFA QSNKNITILV
160 170 180 190 200
QIESQQGVDN VDAIAATEGV DGIFVGPSDL AAALGHLGNA SHPDVQKAIQ
210 220 230 240 250
HIFNRASAHG KPSGILAPVE ADARRYLEWG ATFVAVGSDL GVFRSATQKL

ADTFKK
Length:256
Mass (Da):27,384
Last modified:October 31, 1995 - v2
Checksum:i8E6345EE3F1CFCDB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18997 Genomic DNA. Translation: AAA57929.1.
U00096 Genomic DNA. Translation: AAC76160.1.
AP009048 Genomic DNA. Translation: BAE77173.1.
D90212 Genomic DNA. Translation: BAA14237.1.
PIRiB65102.
RefSeqiNP_417595.1. NC_000913.3.
YP_491314.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC76160; AAC76160; b3126.
BAE77173; BAE77173; BAE77173.
GeneIDi12930493.
947630.
KEGGiecj:Y75_p3048.
eco:b3126.
PATRICi32121666. VBIEscCol129921_3219.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18997 Genomic DNA. Translation: AAA57929.1.
U00096 Genomic DNA. Translation: AAC76160.1.
AP009048 Genomic DNA. Translation: BAE77173.1.
D90212 Genomic DNA. Translation: BAA14237.1.
PIRiB65102.
RefSeqiNP_417595.1. NC_000913.3.
YP_491314.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DXEX-ray1.80A/B1-256[»]
1DXFX-ray2.60A/B1-256[»]
ProteinModelPortaliP23522.
SMRiP23522. Positions 4-256.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-9740N.
IntActiP23522. 9 interactions.
STRINGi511145.b3126.

Proteomic databases

PaxDbiP23522.
PRIDEiP23522.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76160; AAC76160; b3126.
BAE77173; BAE77173; BAE77173.
GeneIDi12930493.
947630.
KEGGiecj:Y75_p3048.
eco:b3126.
PATRICi32121666. VBIEscCol129921_3219.

Organism-specific databases

EchoBASEiEB0016.
EcoGeneiEG10016. garL.

Phylogenomic databases

eggNOGiCOG3836.
HOGENOMiHOG000179750.
InParanoidiP23522.
KOiK01630.
OMAiVRPPCNE.
OrthoDBiEOG6NPM5P.
PhylomeDBiP23522.

Enzyme and pathway databases

UniPathwayiUPA00565; UER00630.
BioCyciEcoCyc:KDGALDOL-MONOMER.
ECOL316407:JW3095-MONOMER.
MetaCyc:KDGALDOL-MONOMER.
BRENDAi4.1.2.20. 2026.

Miscellaneous databases

EvolutionaryTraceiP23522.
PROiP23522.

Gene expression databases

GenevestigatoriP23522.

Family and domain databases

Gene3Di3.20.20.60. 1 hit.
HAMAPiMF_01291. KDGluc_aldolase.
InterProiIPR005000. Aldolase/citrate-lyase_domain.
IPR017648. Dehyd-dGlucarate-aldolase_GarL.
IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
[Graphical view]
PfamiPF03328. HpcH_HpaI. 1 hit.
[Graphical view]
SUPFAMiSSF51621. SSF51621. 1 hit.
TIGRFAMsiTIGR03239. GarL. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. 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(2005) [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(1990) [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(1997) [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(1965)
    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(1999) [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(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEXES WITH MAGNESIUM AND PYRUVATE, SUBUNIT.

Entry informationi

Entry nameiGARL_ECOLI
AccessioniPrimary (citable) accession number: P23522
Secondary accession number(s): Q2M983
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 1991
Last sequence update: October 31, 1995
Last modified: March 31, 2015
This is version 126 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The catalytic mechanism was originally thought to use a phosphate as the catalytic acid, but this was subsequently disputed (PubMed:15996099, PubMed:17881002 and PubMed:18754683).1 Publication

Caution

Was wrongly named 2-dehydro-3-deoxygalactarate aldolase (DDG aldolase or DDGA) in PubMed:10921867. 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.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.