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P39304

- ULAD_ECOLI

UniProt

P39304 - ULAD_ECOLI

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Protein

3-keto-L-gulonate-6-phosphate decarboxylase UlaD

Gene
ulaD, sgaH, yjfV, b4196, JW4154
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Catalyzes the decarboxylation of 3-keto-L-gulonate-6-P into L-xylulose-5-P. Is involved in the anaerobic L-ascorbate utilization.1 Publication

Catalytic activityi

3-dehydro-L-gulonate 6-phosphate = L-xylulose 5-phosphate + CO2.UniRule annotation

Cofactori

Binds 1 magnesium ion per subunit.

Kineticsi

  1. KM=0.67 mM for 3-keto-L-gulonate-6-P1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei11 – 111Substrate
Metal bindingi33 – 331Magnesium
Metal bindingi62 – 621Magnesium
Sitei64 – 641Transition state stabilizer
Sitei67 – 671Transition state stabilizer
Binding sitei192 – 1921Substrate

GO - Molecular functioni

  1. 3-dehydro-L-gulonate-6-phosphate decarboxylase activity Source: EcoCyc
  2. magnesium ion binding Source: EcoCyc
  3. orotidine-5'-phosphate decarboxylase activity Source: InterPro

GO - Biological processi

  1. 'de novo' pyrimidine nucleobase biosynthetic process Source: InterPro
  2. L-ascorbic acid catabolic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Carbohydrate metabolism

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:G7858-MONOMER.
ECOL316407:JW4154-MONOMER.
MetaCyc:G7858-MONOMER.
SABIO-RKP39304.
UniPathwayiUPA00263; UER00378.

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:ulaD
Synonyms:sgaH, yjfV
Ordered Locus Names:b4196, JW4154
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG12496. ulaD.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi33 – 331E → K: Loss of activity. 1 Publication
Mutagenesisi64 – 641K → A: 16% of wild-type activity. 1 Publication
Mutagenesisi67 – 671D → A: 5% of wild-type activity. 1 Publication
Mutagenesisi112 – 1121E → A: 0.5% of wild-type activity. 1 Publication
Mutagenesisi136 – 1361H → A: 5% of wild-type activity. 1 Publication
Mutagenesisi139 – 1391R → V: 17% of wild-type activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 2162163-keto-L-gulonate-6-phosphate decarboxylase UlaDUniRule annotationPRO_0000212103Add
BLAST

Proteomic databases

PRIDEiP39304.

2D gel databases

SWISS-2DPAGEP39304.

Expressioni

Inductioni

Induced by L-ascorbate. Repressed by UlaR.2 Publications

Gene expression databases

GenevestigatoriP39304.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

DIPiDIP-10869N.
IntActiP39304. 1 interaction.
STRINGi511145.b4196.

Structurei

Secondary structure

1
216
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 106
Helixi15 – 2511
Helixi26 – 283
Beta strandi30 – 345
Helixi36 – 427
Helixi45 – 539
Beta strandi57 – 659
Helixi69 – 7810
Beta strandi82 – 876
Helixi92 – 10413
Beta strandi108 – 1136
Helixi119 – 1279
Beta strandi132 – 1365
Helixi139 – 1435
Helixi150 – 16112
Beta strandi165 – 1717
Helixi174 – 1807
Beta strandi186 – 1916
Helixi192 – 1954
Beta strandi197 – 1993
Helixi200 – 21415

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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[»]
ProteinModelPortaliP39304.
SMRiP39304. Positions 2-216.

Miscellaneous databases

EvolutionaryTraceiP39304.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0269.
HOGENOMiHOG000226068.
KOiK03078.
OMAiSHAYETT.
OrthoDBiEOG66B435.
PhylomeDBiP39304.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01267. UlaD.
InterProiIPR023942. 3-keto-L-gulonate6Pdecase_UlaD.
IPR013785. Aldolase_TIM.
IPR001754. OMPdeCOase_dom.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]
PfamiPF00215. OMPdecase. 1 hit.
[Graphical view]
SMARTiSM00934. OMPdecase. 1 hit.
[Graphical view]
SUPFAMiSSF51366. SSF51366. 1 hit.

Sequencei

Sequence statusi: Complete.

P39304-1 [UniParc]FASTAAdd to Basket

« Hide

MSLPMLQVAL DNQTMDSAYE TTRLIAEEVD IIEVGTILCV GEGVRAVRDL    50
KALYPHKIVL ADAKIADAGK ILSRMCFEAN ADWVTVICCA DINTAKGALD 100
VAKEFNGDVQ IELTGYWTWE QAQQWRDAGI GQVVYHRSRD AQAAGVAWGE 150
ADITAIKRLS DMGFKVTVTG GLALEDLPLF KGIPIHVFIA GRSIRDAASP 200
VEAARQFKRS IAELWG 216
Length:216
Mass (Da):23,578
Last modified:February 1, 1995 - v1
Checksum:iEC8490DA1D02D824
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U14003 Genomic DNA. Translation: AAA97092.1.
U00096 Genomic DNA. Translation: AAC77153.1.
AP009048 Genomic DNA. Translation: BAE78197.1.
PIRiS56421.
RefSeqiNP_418617.1. NC_000913.3.
YP_492338.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC77153; AAC77153; b4196.
BAE78197; BAE78197; BAE78197.
GeneIDi12933006.
948714.
KEGGiecj:Y75_p4082.
eco:b4196.
PATRICi32123967. VBIEscCol129921_4328.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U14003 Genomic DNA. Translation: AAA97092.1 .
U00096 Genomic DNA. Translation: AAC77153.1 .
AP009048 Genomic DNA. Translation: BAE78197.1 .
PIRi S56421.
RefSeqi NP_418617.1. NC_000913.3.
YP_492338.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1KV8 X-ray 1.62 A/B 1-216 [» ]
1KW1 X-ray 2.20 A/B 1-216 [» ]
1Q6L X-ray 1.80 A/B 1-216 [» ]
1Q6O X-ray 1.20 A/B 1-216 [» ]
1Q6Q X-ray 1.70 A/B 1-216 [» ]
1Q6R X-ray 1.76 A/B 1-216 [» ]
1SO3 X-ray 1.90 A/B 1-216 [» ]
1SO4 X-ray 1.70 A/B 1-216 [» ]
1SO5 X-ray 1.80 A/B 1-216 [» ]
1SO6 X-ray 1.90 A/B 1-216 [» ]
1XBV X-ray 1.66 A/B 1-216 [» ]
1XBX X-ray 1.81 A/B 1-216 [» ]
1XBY X-ray 1.58 A/B 1-216 [» ]
1XBZ X-ray 1.80 A/B 1-216 [» ]
ProteinModelPortali P39304.
SMRi P39304. Positions 2-216.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-10869N.
IntActi P39304. 1 interaction.
STRINGi 511145.b4196.

2D gel databases

SWISS-2DPAGE P39304.

Proteomic databases

PRIDEi P39304.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC77153 ; AAC77153 ; b4196 .
BAE78197 ; BAE78197 ; BAE78197 .
GeneIDi 12933006.
948714.
KEGGi ecj:Y75_p4082.
eco:b4196.
PATRICi 32123967. VBIEscCol129921_4328.

Organism-specific databases

EchoBASEi EB2389.
EcoGenei EG12496. ulaD.

Phylogenomic databases

eggNOGi COG0269.
HOGENOMi HOG000226068.
KOi K03078.
OMAi SHAYETT.
OrthoDBi EOG66B435.
PhylomeDBi P39304.

Enzyme and pathway databases

UniPathwayi UPA00263 ; UER00378 .
BioCyci EcoCyc:G7858-MONOMER.
ECOL316407:JW4154-MONOMER.
MetaCyc:G7858-MONOMER.
SABIO-RK P39304.

Miscellaneous databases

EvolutionaryTracei P39304.
PROi P39304.

Gene expression databases

Genevestigatori P39304.

Family and domain databases

Gene3Di 3.20.20.70. 1 hit.
HAMAPi MF_01267. UlaD.
InterProi IPR023942. 3-keto-L-gulonate6Pdecase_UlaD.
IPR013785. Aldolase_TIM.
IPR001754. OMPdeCOase_dom.
IPR011060. RibuloseP-bd_barrel.
[Graphical view ]
Pfami PF00215. OMPdecase. 1 hit.
[Graphical view ]
SMARTi SM00934. OMPdecase. 1 hit.
[Graphical view ]
SUPFAMi SSF51366. SSF51366. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. 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.

Entry informationi

Entry nameiULAD_ECOLI
AccessioniPrimary (citable) accession number: P39304
Secondary accession number(s): Q2M6A9
Entry historyi
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 statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.

Keywords - Technical termi

3D-structure, Complete proteome, 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

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