SubmitCancel

Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

P23522

- GARL_ECOLI

UniProt

P23522 - GARL_ECOLI

(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Protein

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

Gene
garL, yhaF, b3126, JW3095
Organism
Escherichia coli (strain K12)
Status
Reviewed - 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

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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei50 – 501Proton acceptor By similarity
Sitei75 – 751Transition state stabilizer By similarity
Sitei89 – 891Increases basicity of active site His By 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. cellular aromatic compound metabolic process Source: InterPro
  2. D-glucarate catabolic process Source: EcoCyc
  3. galactarate catabolic process Source: EcoCyc
  4. 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.
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: Chromosome, UP000000625: 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 aldolaseUniRule annotationPRO_0000207093Add
BLAST

Proteomic databases

PaxDbiP23522.
PRIDEiP23522.

PTM databases

PhosSiteiP0809389.

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 – 157
Beta strandi20 – 256
Helixi30 – 367
Beta strandi42 – 5211
Helixi55 – 6410
Turni65 – 673
Beta strandi69 – 757
Beta strandi77 – 793
Helixi81 – 899
Beta strandi94 – 985
Helixi103 – 1119
Turni116 – 1183
Beta strandi125 – 1273
Helixi128 – 1303
Turni131 – 1344
Helixi138 – 1425
Beta strandi147 – 1526
Helixi155 – 1595
Helixi161 – 1655
Beta strandi172 – 1754
Helixi177 – 1837
Helixi193 – 20816
Beta strandi213 – 2164
Helixi220 – 2289
Beta strandi233 – 2386
Helixi239 – 25416

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP23522.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG3836.
HOGENOMiHOG000179750.
KOiK01630.
OMAiHAPNDIT.
OrthoDBiEOG6NPM5P.
PhylomeDBiP23522.

Family and domain databases

Gene3Di3.20.20.60. 1 hit.
HAMAPiMF_01291. KDGluc_aldolase.
InterProiIPR005000. Aldehyde-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

MNNDVFPNKF KAALAAKQVQ IGCWSALSNP ISTEVLGLAG FDWLVLDGEH    50
APNDISTFIP QLMALKGSAS APVVRVPTNE PVIIKRLLDI GFYNFLIPFV 100
ETKEEAELAV ASTRYPPEGI RGVSVSHRAN MFGTVADYFA QSNKNITILV 150
QIESQQGVDN VDAIAATEGV DGIFVGPSDL AAALGHLGNA SHPDVQKAIQ 200
HIFNRASAHG KPSGILAPVE ADARRYLEWG ATFVAVGSDL GVFRSATQKL 250
ADTFKK 256
Length:256
Mass (Da):27,384
Last modified:November 1, 1995 - v2
Checksum:i8E6345EE3F1CFCDB
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
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 .
PIRi B65102.
RefSeqi NP_417595.1. NC_000913.3.
YP_491314.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1DXE X-ray 1.80 A/B 1-256 [» ]
1DXF X-ray 2.60 A/B 1-256 [» ]
ProteinModelPortali P23522.
SMRi P23522. Positions 4-256.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-9740N.
IntActi P23522. 9 interactions.
STRINGi 511145.b3126.

PTM databases

PhosSitei P0809389.

Proteomic databases

PaxDbi P23522.
PRIDEi P23522.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC76160 ; AAC76160 ; b3126 .
BAE77173 ; BAE77173 ; BAE77173 .
GeneIDi 12930493.
947630.
KEGGi ecj:Y75_p3048.
eco:b3126.
PATRICi 32121666. VBIEscCol129921_3219.

Organism-specific databases

EchoBASEi EB0016.
EcoGenei EG10016. garL.

Phylogenomic databases

eggNOGi COG3836.
HOGENOMi HOG000179750.
KOi K01630.
OMAi HAPNDIT.
OrthoDBi EOG6NPM5P.
PhylomeDBi P23522.

Enzyme and pathway databases

UniPathwayi UPA00565 ; UER00630 .
BioCyci EcoCyc:KDGALDOL-MONOMER.
ECOL316407:JW3095-MONOMER.
MetaCyc:KDGALDOL-MONOMER.

Miscellaneous databases

EvolutionaryTracei P23522.
PROi P23522.

Gene expression databases

Genevestigatori P23522.

Family and domain databases

Gene3Di 3.20.20.60. 1 hit.
HAMAPi MF_01291. KDGluc_aldolase.
InterProi IPR005000. Aldehyde-lyase_domain.
IPR017648. Dehyd-dGlucarate-aldolase_GarL.
IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
[Graphical view ]
Pfami PF03328. HpcH_HpaI. 1 hit.
[Graphical view ]
SUPFAMi SSF51621. SSF51621. 1 hit.
TIGRFAMsi TIGR03239. GarL. 1 hit.
ProtoNeti Search...

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(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.

Entry informationi

Entry nameiGARL_ECOLI
AccessioniPrimary (citable) accession number: P23522
Secondary accession number(s): Q2M983
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1991
Last sequence update: November 1, 1995
Last modified: June 11, 2014
This is version 120 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 (1 Publication) thought to use a phosphate as the catalytic acid, but this was subsequently disputed (PubMed:15996099, PubMed:17881002 and PubMed:18754683).

Caution

Was wrongly named 2-dehydro-3-deoxygalactarate aldolase (DDG aldolase or DDGA) in 1 Publication. 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.

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