5-keto-4-deoxy-D-glucarate aldolase - Escherichia coli (strain K12)

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P23522 (GARL_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 112. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended 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

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	256 AA.
Sequence status	Complete.
Protein existence	Evidence 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). HAMAP-Rule MF_01291
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: K_M=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.

Ontologies

Keywords
Ligand	Cobalt Iron Magnesium Manganese Metal-binding
Molecular function	Lyase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	D-galactarate catabolic process Inferred from direct assay Ref.4. Source: EcoCyc D-glucarate catabolic process Inferred from direct assay Ref.4. Source: EcoCyc cellular aromatic compound metabolic process Inferred from electronic annotation. Source: InterPro
Cellular_component	cytoplasm Inferred from direct assay Ref.4. Source: EcoliWiki
Molecular_function	2-dehydro-3-deoxyglucarate aldolase activity Inferred from direct assay Ref.4. Source: EcoliWiki magnesium ion binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 256

256

5-keto-4-deoxy-D-glucarate aldolase HAMAP-Rule MF_01291

PRO_0000207093

Sites

Active site

Proton acceptor By similarity

Metal binding

153

Magnesium

Metal binding

179

Magnesium

Binding site

151

Substrate

Binding site

178

Substrate; via amide nitrogen

Binding site

179

Substrate

Site

Transition state stabilizer By similarity

Site

Increases basicity of active site His By similarity

Secondary structure

256

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P23522 [UniParc].

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

FASTA

256

27,384

        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' referencesShow '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 277:1453-1474(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.

PIR

B65102.

RefSeq

NP_417595.1. NC_000913.2.
YP_491314.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P23522.

SMR

P23522. Positions 4-256.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9740N.

IntAct

P23522. 8 interactions.

STRING

511145.b3126.

PTM databases

PhosSite

P0809389.

Proteomic databases

PaxDb

P23522.

PRIDE

P23522.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76160; AAC76160; b3126.
BAE77173; BAE77173; BAE77173.

GeneID

12930493.
947630.

KEGG

ecj:Y75_p3048.
eco:b3126.

PATRIC

32121666. VBIEscCol129921_3219.

Organism-specific databases

EchoBASE

EB0016.

EcoGene

EG10016. garL.

Phylogenomic databases

eggNOG

COG3836.

HOGENOM

HOG000179750.

K01630.

OMA

CNEPVII.

ProtClustDB

PRK10558.

Enzyme and pathway databases

BioCyc

EcoCyc:KDGALDOL-MONOMER.
ECOL316407:JW3095-MONOMER.
MetaCyc:KDGALDOL-MONOMER.

UniPathway

UPA00565; UER00630.

Gene expression databases

Genevestigator

P23522.

Family and domain databases

Gene3D

3.20.20.60. 1 hit.

HAMAP

MF_01291. KDGluc_aldolase.

InterPro

IPR005000. Aldehyde-lyase_domain.
IPR017648. Dehyd-dGlucarate-aldolase_GarL.
IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
[Graphical view]

Pfam

PF03328. HpcH_HpaI. 1 hit.
[Graphical view]

SUPFAM

SSF51621. Pyrv/PenolPyrv_Kinase_cat. 1 hit.

TIGRFAMs

TIGR03239. GarL. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P23522.

Entry information

Entry name

GARL_ECOLI

Accession

Primary (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:	May 29, 2013
This is version 112 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

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

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

PTM databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents