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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

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.

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 UlaDPRO_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.3 Publications

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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP39304.

Family & Domainsi

Sequence similaritiesi

Belongs to the HPS/KGPDC family. KGPDC subfamily.Curated

Phylogenomic databases

eggNOGiCOG0269.
HOGENOMiHOG000226068.
InParanoidiP39304.
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

        10         20         30         40         50
MSLPMLQVAL DNQTMDSAYE TTRLIAEEVD IIEVGTILCV GEGVRAVRDL
60 70 80 90 100
KALYPHKIVL ADAKIADAGK ILSRMCFEAN ADWVTVICCA DINTAKGALD
110 120 130 140 150
VAKEFNGDVQ IELTGYWTWE QAQQWRDAGI GQVVYHRSRD AQAAGVAWGE
160 170 180 190 200
ADITAIKRLS DMGFKVTVTG GLALEDLPLF KGIPIHVFIA GRSIRDAASP
210
VEAARQFKRS IAELWG
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.
InParanoidi P39304.
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: October 29, 2014
This is version 122 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