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

Contribute

Send feedback

Read comments (?) or add your own

P39304 (ULAD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 113. History...

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

Documents (4) |

Third-party data

text xml rdf/xml gff fasta

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

Names and origin

Protein names

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 names

Name:	ulaD
Synonyms:	sgaH, yjfV
Ordered Locus Names:	b4196, JW4154

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	216 AA.
Sequence status	Complete.
Protein existence	Evidence 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. HAMAP-Rule MF_01267
Sequence similarities	Belongs to the HPS/KGPDC family. KGPDC subfamily.
Biophysicochemical properties	Kinetic parameters: K_M=0.67 mM for 3-keto-L-gulonate-6-P Ref.9

Ontologies

Keywords
Biological process	Carbohydrate metabolism
Ligand	Magnesium Metal-binding
Molecular function	Decarboxylase Lyase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	'de novo' pyrimidine nucleobase biosynthetic process Inferred from electronic annotation. Source: InterPro L-ascorbic acid catabolic process Inferred from expression pattern Ref.8. Source: EcoCyc
Molecular_function	3-dehydro-L-gulonate-6-phosphate decarboxylase activity Inferred from direct assay Ref.6. Source: EcoCyc magnesium ion binding Inferred from direct assay Ref.11. Source: EcoCyc orotidine-5'-phosphate decarboxylase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 216

216

3-keto-L-gulonate-6-phosphate decarboxylase UlaD HAMAP-Rule MF_01267

PRO_0000212103

Sites

Metal binding

Magnesium

Metal binding

Magnesium

Binding site

Substrate

Binding site

192

Substrate

Site

Transition state stabilizer

Site

Transition state stabilizer

Experimental info

Mutagenesis

E → K: Loss of activity. Ref.9

Mutagenesis

K → A: 16% of wild-type activity. Ref.9

Mutagenesis

D → A: 5% of wild-type activity. Ref.9

Mutagenesis

112

E → A: 0.5% of wild-type activity. Ref.9

Mutagenesis

136

H → A: 5% of wild-type activity. Ref.9

Mutagenesis

139

R → V: 17% of wild-type activity. Ref.9

Secondary structure

216

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P39304 [UniParc].

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

FASTA

216

23,578

        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' referencesShow '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 277:1453-1474(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.

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.

PIR

S56421.

RefSeq

NP_418617.1. NC_000913.2.
YP_492338.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P39304.

SMR

P39304. Positions 2-216.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10869N.

IntAct

P39304. 1 interaction.

STRING

511145.b4196.

2D gel databases

SWISS-2DPAGE

P39304.

Proteomic databases

PRIDE

P39304.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC77153; AAC77153; b4196.
BAE78197; BAE78197; BAE78197.

GeneID

12933006.
948714.

KEGG

ecj:Y75_p4082.
eco:b4196.

PATRIC

32123967. VBIEscCol129921_4328.

Organism-specific databases

EchoBASE

EB2389.

EcoGene

EG12496. ulaD.

Phylogenomic databases

eggNOG

COG0269.

HOGENOM

HOG000226068.

K03078.

OMA

IFIAGRS.

ProtClustDB

PRK13306.

Enzyme and pathway databases

BioCyc

EcoCyc:G7858-MONOMER.
ECOL316407:JW4154-MONOMER.
MetaCyc:G7858-MONOMER.

SABIO-RK

P39304.

UniPathway

UPA00263; UER00378.

Gene expression databases

Genevestigator

P39304.

Family and domain databases

Gene3D

3.20.20.70. 1 hit.

HAMAP

MF_01267. UlaD.

InterPro

IPR023942. 3-keto-L-gulonate6Pdecase_UlaD.
IPR013785. Aldolase_TIM.
IPR001754. OMPdeCOase_dom.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]

Pfam

PF00215. OMPdecase. 1 hit.
[Graphical view]

SMART

SM00934. OMPdecase. 1 hit.
[Graphical view]

SUPFAM

SSF51366. RibP_bind_barrel. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P39304.

Entry information

Entry name

ULAD_ECOLI

Accession

Primary (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 1, 2013
This is version 113 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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2D gel 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