D-galactonate dehydratase - Escherichia coli (strain K12)

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Q6BF17 (DGOD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 79. History...

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

Documents (3) |

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:
D-galactonate dehydratase
Short name=GalD
EC=4.2.1.6

Gene names

Name:	dgoD
Synonyms:	yidU
Ordered Locus Names:	b4478, JW5629

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	382 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the dehydration of D-galactonate to 2-keto-3-deoxy-D-galactonate. Ref.5 Ref.7
Catalytic activity	D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H₂O. HAMAP-Rule MF_01289
Cofactor	Binds 1 magnesium ion per subunit By similarity.
Pathway	Carbohydrate acid metabolism; D-galactonate degradation; D-glyceraldehyde 3-phosphate and pyruvate from D-galactonate: step 1/3. Ref.5
Induction	Induced by galactonate, but not by glycerol, gluconate or galactose. Repressed by glucose. Ref.5
Miscellaneous	Reaction proceeds via an anti dehydration. HAMAP-Rule MF_01289
Sequence similarities	Belongs to the mandelate racemase/muconate lactonizing enzyme family. GalD subfamily.
Biophysicochemical properties	Kinetic parameters: K_M=1.5 mM for D-galactonate Ref.7
Sequence caution	The sequence AAA62044.1 differs from that shown. Reason: Frameshift at position 1. The frameshift in position 1 caused the prediction of an ORF that fused dgoA and dgoD.

Ontologies

Keywords
Ligand	Magnesium Metal-binding
Molecular function	Lyase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	D-galactonate catabolic process Inferred from mutant phenotype Ref.6. Source: EcoCyc cellular amino acid catabolic process Inferred from electronic annotation. Source: InterPro
Molecular_function	galactonate dehydratase activity Inferred from electronic annotation. Source: HAMAP 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 – 382

382

D-galactonate dehydratase HAMAP-Rule MF_01289

PRO_0000171259

Sites

Active site

185

Proton donor

Active site

285

Proton acceptor

Metal binding

183

Magnesium By similarity

Metal binding

209

Magnesium By similarity

Metal binding

235

Magnesium By similarity

Site

258

Increases basicity of active site His By similarity

Site

310

Transition state stabilizer

Experimental info

Mutagenesis

185

H → N or Q: Loss of activity. Ref.7

Mutagenesis

285

H → N: Loss of activity. Ref.7

Mutagenesis

310

E → Q: Loss of activity. Ref.7

Sequence conflict

137

E → Q in AAA62044. Ref.1

Sequences

Sequence

Length

Mass (Da)

Tools

Q6BF17 [UniParc].

Last modified August 16, 2004. Version 1.
Checksum: B38D4E0B95FD7041
Show »

FASTA

382

42,523

        10         20         30         40         50         60 
MKITKITTYR LPPRWMFLKI ETDEGVVGWG EPVIEGRART VEAAVHELGD YLIGQDPSRI 

        70         80         90        100        110        120 
NDLWQVMYRA GFYRGGPILM SAIAGIDQAL WDIKGKVLNA PVWQLMGGLV RDKIKAYSWV 

       130        140        150        160        170        180 
GGDRPADVID GIKTLREIGF DTFKLNGCEE LGLIDNSRAV DAAVNTVAQI REAFGNQIEF 

       190        200        210        220        230        240 
GLDFHGRVSA PMAKVLIKEL EPYRPLFIEE PVLAEQAEYY PKLAAQTHIP LAAGERMFSR 

       250        260        270        280        290        300 
FDFKRVLEAG GISILQPDLS HAGGITECYK IAGMAEAYDV TLAPHCPLGP IALAACLHID 

       310        320        330        340        350        360 
FVSYNAVLQE QSMGIHYNKG AELLDFVKNK EDFSMVGGFF KPLTKPGLGV EIDEAKVIEF 

       370        380 
SKNAPDWRNP LWRHEDNSVA EW

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication." Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R. Genomics 16:551-561(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[2]	"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.
[3]	"Escherichia coli K-12: a cooperatively developed annotation snapshot -- 2005." Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R., Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T., Mori H., Perna N.T., Plunkett G. III, Rudd K.E., Serres M.H., Thomas G.H., Thomson N.R., Wishart D., Wanner B.L. Nucleic Acids Res. 34:1-9(2006) [PubMed] [Europe PMC] [Abstract] Cited for: SEQUENCE REVISION.
[4]	"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.
[5]	"D-galactonate utilisation by enteric bacteria. The catabolic pathway in Escherichia coli." Deacon J., Cooper R.A. FEBS Lett. 77:201-205(1977) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, PATHWAY, INDUCTION. Strain: K12.
[6]	"The utilisation of D-galactonate and D-2-oxo-3-deoxygalactonate by Escherichia coli K-12. Biochemical and genetical studies." Cooper R.A. Arch. Microbiol. 118:199-206(1978) [PubMed] [Europe PMC] [Abstract] Cited for: REPRESSION BY GLUCOSE, GENETIC LOCATION. Strain: K12.
[7]	"Evolution of enzymatic activities in the enolase superfamily: identification of a 'new' general acid catalyst in the active site of D-galactonate dehydratase from Escherichia coli." Wieczorek S.J., Kalivoda K.A., Clifton J.G., Ringe D., Petsko G.A., Gerlt J.A. J. Am. Chem. Soc. 121:4540-4541(1999) Cited for: FUNCTION, KINETIC PARAMETERS, CATALYTIC MECHANISM, REACTION STEREOCHEMISTRY, MUTAGENESIS OF HIS-185; HIS-285 AND GLU-310.

Cross-references

Sequence databases
EMBL GenBank DDBJ	L10328 Genomic DNA. Translation: AAA62044.1. Frameshift. U00096 Genomic DNA. Translation: AAT48197.1. AP009048 Genomic DNA. Translation: BAE77602.1.
PIR	E65171.
RefSeq	YP_026237.1. NC_000913.2. YP_491743.1. NC_007779.1.
3D structure databases
ProteinModelPortal	Q6BF17.
SMR	Q6BF17. Positions 1-382.
ModBase	Search...
Protein-protein interaction databases
STRING	511145.b4478.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAT48197; AAT48197; b4478. BAE77602; BAE77602; BAE77602.
GeneID	12931852. 2847765.
KEGG	ecj:Y75_p3481. eco:b4478.
PATRIC	32122879. VBIEscCol129921_3815.
Organism-specific databases
EchoBASE	EB4309.
EcoGene	EG20050. dgoD.
Phylogenomic databases
eggNOG	COG4948.
HOGENOM	HOG000113756.
KO	K01684.
OMA	RSAFGNT.
ProtClustDB	PRK14017.
Enzyme and pathway databases
BioCyc	EcoCyc:GALACTONATE-DEHYDRATASE-MONOMER. ECOL316407:JW5629-MONOMER. MetaCyc:GALACTONATE-DEHYDRATASE-MONOMER.
UniPathway	UPA00081; UER00518.
Gene expression databases
Genevestigator	Q6BF17.
Family and domain databases
HAMAP	MF_01289. Galacton_dehydrat.
InterPro	IPR023592. Galactonate_deHydtase. IPR018110. Mandel_Rmase/mucon_lact_enz_CS. IPR013342. Mandelate_racemase_C. IPR013341. Mandelate_racemase_N. IPR001354. MR_MLE. [Graphical view]
PANTHER	PTHR13794. PTHR13794. 1 hit.
Pfam	PF02746. MR_MLE_N. 1 hit. [Graphical view]
SMART	SM00922. MR_MLE. 1 hit. [Graphical view]
PROSITE	PS00908. MR_MLE_1. 1 hit. PS00909. MR_MLE_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DGOD_ECOLI

Accession

Primary (citable) accession number: Q6BF17
Secondary accession number(s): P31458, Q2M804

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 23, 2004
Last sequence update:	August 16, 2004
Last modified:	May 1, 2013
This is version 79 of the entry and version 1 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

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

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents