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P39304 (ULAD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 120. 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:
3-keto-L-gulonate-6-phosphate decarboxylase UlaD

EC=4.1.1.85
Alternative name(s):
3-dehydro-L-gulonate-6-phosphate decarboxylase
KGPDC
L-ascorbate utilization protein D
Gene names
Name:ulaD
Synonyms:sgaH, yjfV
Ordered Locus Names:b4196, JW4154
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length216 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the decarboxylation of 3-keto-L-gulonate-6-P into L-xylulose-5-P. Is involved in the anaerobic L-ascorbate utilization. Ref.6

Catalytic activity

3-dehydro-L-gulonate 6-phosphate = L-xylulose 5-phosphate + CO2. HAMAP-Rule MF_01267

Cofactor

Binds 1 magnesium ion per subunit.

Pathway

Cofactor degradation; L-ascorbate degradation; D-xylulose 5-phosphate from L-ascorbate: step 2/4. HAMAP-Rule MF_01267

Subunit structure

Homodimer. Ref.11

Induction

Induced by L-ascorbate. Repressed by UlaR. Ref.7 Ref.8

Miscellaneous

The reaction mechanism proceeds via the formation of a Mg2+ ion-stabilized 1,2-cis-enediolate intermediate. Water molecules competitively shuttle protons from the side chains of His-136 and Arg-139 to alternate faces of this intermediate. The active site is located at the interface of the component polypeptides.

Sequence similarities

Belongs to the HPS/KGPDC family. KGPDC subfamily.

Biophysicochemical properties

Kinetic parameters:

KM=0.67 mM for 3-keto-L-gulonate-6-P Ref.9

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 2162163-keto-L-gulonate-6-phosphate decarboxylase UlaD HAMAP-Rule MF_01267
PRO_0000212103

Sites

Metal binding331Magnesium
Metal binding621Magnesium
Binding site111Substrate
Binding site1921Substrate
Site641Transition state stabilizer
Site671Transition state stabilizer

Experimental info

Mutagenesis331E → K: Loss of activity. Ref.9
Mutagenesis641K → A: 16% of wild-type activity. Ref.9
Mutagenesis671D → A: 5% of wild-type activity. Ref.9
Mutagenesis1121E → A: 0.5% of wild-type activity. Ref.9
Mutagenesis1361H → A: 5% of wild-type activity. Ref.9
Mutagenesis1391R → V: 17% of wild-type activity. Ref.9

Secondary structure

........................................ 216
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P39304 [UniParc].

Last modified February 1, 1995. Version 1.
Checksum: EC8490DA1D02D824

FASTA21623,578
        10         20         30         40         50         60 
MSLPMLQVAL DNQTMDSAYE TTRLIAEEVD IIEVGTILCV GEGVRAVRDL KALYPHKIVL 

        70         80         90        100        110        120 
ADAKIADAGK ILSRMCFEAN ADWVTVICCA DINTAKGALD VAKEFNGDVQ IELTGYWTWE 

       130        140        150        160        170        180 
QAQQWRDAGI GQVVYHRSRD AQAAGVAWGE ADITAIKRLS DMGFKVTVTG GLALEDLPLF 

       190        200        210 
KGIPIHVFIA GRSIRDAASP VEAARQFKRS IAELWG 

« Hide

References

« Hide 'large scale' references
[1]"Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
Nucleic Acids Res. 23:2105-2119(1995) [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 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[3]"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.
[4]"Novel phosphotransferases system genes revealed by bacterial genome analysis: operons encoding homologues of sugar-specific permease domains of the phosphotransferase system and pentose catabolic enzymes."
Reizer J., Charbit A., Reizer A., Saier M.H. Jr.
Genome Sci. Technol. 1:53-75(1996)
Cited for: DISCUSSION OF SEQUENCE.
[5]"Is the ribulose monophosphate pathway widely distributed in bacteria?"
Reizer J., Reizer A., Saier M.H. Jr.
Microbiology 143:2519-2520(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: DISCUSSION OF SEQUENCE.
[6]"Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons."
Yew W.S., Gerlt J.A.
J. Bacteriol. 184:302-306(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, ROLE IN L-ASCORBATE UTILIZATION.
Strain: K12 / MG1655 / ATCC 47076.
[7]"The gene yjfQ encodes the repressor of the yjfR-X regulon (ula), which is involved in L-ascorbate metabolism in Escherichia coli."
Campos E., Aguilar J., Baldoma L., Badia J.
J. Bacteriol. 184:6065-6068(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: TRANSCRIPTIONAL REGULATION.
[8]"Regulation of expression of the divergent ulaG and ulaABCDEF operons involved in L-ascorbate dissimilation in Escherichia coli."
Campos E., Baldoma L., Aguilar J., Badia J.
J. Bacteriol. 186:1720-1728(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: TRANSCRIPTIONAL REGULATION.
[9]"Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: mechanistic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase."
Yew W.S., Wise E.L., Rayment I., Gerlt J.A.
Biochemistry 43:6427-6437(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF GLU-33; LYS-64; ASP-67; GLU-112; HIS-136 AND ARG-139, KINETIC PARAMETERS, REACTION STEREOCHEMISTRY.
[10]"Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: enhancing the promiscuous D-arabino-hex-3-ulose 6-phosphate synthase reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase."
Yew W.S., Akana J., Wise E.L., Rayment I., Gerlt J.A.
Biochemistry 44:1807-1815(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS.
[11]"Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase."
Wise E., Yew W.S., Babbitt P.C., Gerlt J.A., Rayment I.
Biochemistry 41:3861-3869(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.62 ANGSTROMS) OF COMPLEXES WITH MAGNESIUM; PHOSPHATE AND L-GULONATE-6-PHOSPHATE, SUBUNIT.
Strain: K12 / MG1655 / ATCC 47076.
[12]"Structural evidence for a 1,2-enediolate intermediate in the reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily."
Wise E.L., Yew W.S., Gerlt J.A., Rayment I.
Biochemistry 42:12133-12142(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.2 ANGSTROMS) OF COMPLEXES WITH L-GULONATE 6-PHOSPHATE; L-THREONOHYDROXAMATE 4-PHOSPHATE; L-XYLITOL 5-PHOSPHATE AND L-XYLULOSE 5-PHOSPHATE.
Strain: K12 / MG1655 / ATCC 47076.
[13]"Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: crystallographic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase."
Wise E.L., Yew W.S., Gerlt J.A., Rayment I.
Biochemistry 43:6438-6446(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF MUTANTS ALA-64; ALA-136; GLN-112 AND GLN-112/ALA-136 IN COMPLEX WITH L-THREONOHYDROXAMATE 4-PHOSPHATE, REACTION MECHANISM.
[14]"Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: structural basis for catalytic promiscuity in wild-type and designed mutants of 3-keto-L-gulonate 6-phosphate decarboxylase."
Wise E.L., Yew W.S., Akana J., Gerlt J.A., Rayment I.
Biochemistry 44:1816-1823(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF NATIVE PROTEIN IN COMPLEX WITH D-RIBULOSE 5-PHOSPHATE; MUTANTS ASP-112/ALA-169 AND ASP-11/VAL-139/ALA-169 IN COMPLEX WITH D-RIBULOSE 5-PHOSPHATE AND MUTANT ASP-11/VAL-139/ALA-169 IN COMPLEX WITH L-XYLULOSE 5-PHOSPHATE.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U14003 Genomic DNA. Translation: AAA97092.1.
U00096 Genomic DNA. Translation: AAC77153.1.
AP009048 Genomic DNA. Translation: BAE78197.1.
PIRS56421.
RefSeqNP_418617.1. NC_000913.3.
YP_492338.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1KV8X-ray1.62A/B1-216[»]
1KW1X-ray2.20A/B1-216[»]
1Q6LX-ray1.80A/B1-216[»]
1Q6OX-ray1.20A/B1-216[»]
1Q6QX-ray1.70A/B1-216[»]
1Q6RX-ray1.76A/B1-216[»]
1SO3X-ray1.90A/B1-216[»]
1SO4X-ray1.70A/B1-216[»]
1SO5X-ray1.80A/B1-216[»]
1SO6X-ray1.90A/B1-216[»]
1XBVX-ray1.66A/B1-216[»]
1XBXX-ray1.81A/B1-216[»]
1XBYX-ray1.58A/B1-216[»]
1XBZX-ray1.80A/B1-216[»]
ProteinModelPortalP39304.
SMRP39304. Positions 2-216.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-10869N.
IntActP39304. 1 interaction.
STRING511145.b4196.

2D gel databases

SWISS-2DPAGEP39304.

Proteomic databases

PRIDEP39304.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC77153; AAC77153; b4196.
BAE78197; BAE78197; BAE78197.
GeneID12933006.
948714.
KEGGecj:Y75_p4082.
eco:b4196.
PATRIC32123967. VBIEscCol129921_4328.

Organism-specific databases

EchoBASEEB2389.
EcoGeneEG12496. ulaD.

Phylogenomic databases

eggNOGCOG0269.
HOGENOMHOG000226068.
KOK03078.
OMASHAYETT.
OrthoDBEOG66B435.
PhylomeDBP39304.

Enzyme and pathway databases

BioCycEcoCyc:G7858-MONOMER.
ECOL316407:JW4154-MONOMER.
MetaCyc:G7858-MONOMER.
SABIO-RKP39304.
UniPathwayUPA00263; UER00378.

Gene expression databases

GenevestigatorP39304.

Family and domain databases

Gene3D3.20.20.70. 1 hit.
HAMAPMF_01267. UlaD.
InterProIPR023942. 3-keto-L-gulonate6Pdecase_UlaD.
IPR013785. Aldolase_TIM.
IPR001754. OMPdeCOase_dom.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]
PfamPF00215. OMPdecase. 1 hit.
[Graphical view]
SMARTSM00934. OMPdecase. 1 hit.
[Graphical view]
SUPFAMSSF51366. SSF51366. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP39304.
PROP39304.

Entry information

Entry nameULAD_ECOLI
AccessionPrimary (citable) accession number: P39304
Secondary accession number(s): Q2M6A9
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: May 14, 2014
This is version 120 of the entry and version 1 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