P0A9J4 (PANE_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
2-dehydropantoate 2-reductase
EC=1.1.1.169

Alternative name(s):
Ketopantoate reductase
Short name=KPA reductase
Short name=KPR

Gene names

Name:	panE
Synonyms:	apbA
Ordered Locus Names:	b0425, JW0415

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	303 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the NADPH-dependent reduction of ketopantoate into pantoic acid.
Catalytic activity	(R)-pantoate + NADP+ = 2-dehydropantoate + NADPH.
Pathway	Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantoate from 3-methyl-2-oxobutanoate: step 2/2.
Subunit structure	Monomer. Ref.9
Subcellular location	Cytoplasm Potential.
Sequence similarities	Belongs to the ketopantoate reductase family.
Biophysicochemical properties	Kinetic parameters: KM=30 µM for ketopantoate Ref.6 Ref.9 Ref.12 KM=7.3 µM for NADPH
Mass spectrometry	Molecular mass is 33976 Da from positions 1 - 303. Determined by ESI. Ref.9

Ontologies

Keywords
Biological process	Pantothenate biosynthesis
Cellular component	Cytoplasm
Ligand	NADP
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	pantothenate biosynthetic process from valine Inferred from mutant phenotype PubMed 10553653. Source: EcoCyc
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	2-dehydropantoate 2-reductase activity Inferred from direct assay Ref.5. Source: EcoCyc NADP binding Inferred from direct assay Ref.5. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 303

303

2-dehydropantoate 2-reductase

PRO_0000157301

Regions

Nucleotide binding

7 – 12

6

NADP

Sites

Active site

176

1

Proton donor

Binding site

31

1

NADP; via amide nitrogen

Binding site

98

1

NADP; via amide nitrogen

Binding site

98

1

Substrate

Binding site

122

1

NADP; via amide nitrogen and carbonyl oxygen

Binding site

180

1

Substrate

Binding site

184

1

Substrate

Binding site

194

1

Substrate

Binding site

241

1

Substrate

Binding site

244

1

Substrate

Binding site

256

1

NADP

Experimental info

Mutagenesis

31

1

R → A: Increases KM for NADP 4-fold. Ref.8

Mutagenesis

72

1

K → A: Increases KM for NADP 10-fold. Ref.12

Mutagenesis

98

1

N → A: Increases KM for ketopantoate 140-fold. Strongly decreases catalytic activity. Ref.8 Ref.11

Mutagenesis

176

1

K → A: Increases KM for ketopantoate 1400-fold. Decreases Vmax 230-fold. Loss of activity; when associated with A-256. Ref.6 Ref.11

Mutagenesis

244

1

S → A: Increases KM for ketopantoate 230-fold. Ref.12

Mutagenesis

256

1

E → A: Increases KM for ketopantoate 1100-fold. Decreases Vmax 40-fold. Loss of activity; when associated with A-176. Ref.6 Ref.11

Secondary structure

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303

Helix Strand Turn

Details...

Beta strand

2 – 6

5

Helix

10 – 21

12

Beta strand

25 – 29

5

Beta strand

35 – 42

8

Beta strand

44 – 46

3

Beta strand

48 – 56

9

Helix

58 – 62

5

Beta strand

65 – 69

5

Helix

73 – 75

3

Helix

76 – 84

9

Beta strand

93 – 96

4

Beta strand

98 – 100

3

Helix

104 – 106

3

Beta strand

113 – 118

6

Beta strand

121 – 125

5

Beta strand

128 – 133

6

Beta strand

137 – 143

7

Helix

144 – 146

3

Helix

151 – 157

7

Beta strand

163 – 165

3

Turn

167 – 169

3

Helix

170 – 189

20

Helix

194 – 199

6

Helix

201 – 218

18

Helix

224 – 237

14

Turn

238 – 240

3

Helix

244 – 250

7

Helix

257 – 259

3

Helix

261 – 271

11

Helix

276 – 290

15

Sequences

	Sequence		Length	Mass (Da)
	P0A9J4 [UniParc]. Last modified July 19, 2005. Version 1. Checksum: ED7027BFE6F86D6F	FASTA	303	33,871
	10 20 30 40 50 60 MKITVLGCGA LGQLWLTALC KQGHEVQGWL RVPQPYCSVN LVETDGSIFN ESLTANDPDF 70 80 90 100 110 120 LATSDLLLVT LKAWQVSDAV KSLASTLPVT TPILLIHNGM GTIEELQNIQ QPLLMGTTTH 130 140 150 160 170 180 AARRDGNVII HVANGITHIG PARQQDGDYS YLADILQTVL PDVAWHNNIR AELWRKLAVN 190 200 210 220 230 240 CVINPLTAIW NCPNGELRHH PQEIMQICEE VAAVIEREGH HTSAEDLRDY VMQVIDATAE 250 260 270 280 290 300 NISSMLQDIR ALRHTEIDYI NGFLLRRARA HGIAVPENTR LFEMVKRKES EYERIGTGLP RPW

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence of minutes 4-25 of Escherichia coli." Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W. Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases 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]	"The biosynthesis of thiamin in Escherichia coli K-12: structural genes for thiamin biosynthetic enzymes (thiCEFGH and thiJ) and function of the thiE gene product (thiamin phosphate synthase [E.C. 2.5.1.3])." Backstrom A.D. Thesis (1996), Cornell University, United States Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 180-303. Strain: K12.
[5]	"Kinetic and mechanistic analysis of the E. coli panE-encoded ketopantoate reductase." Zheng R., Blanchard J.S. Biochemistry 39:3708-3717(2000) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION. Strain: K12.
[6]	"Identification of active site residues in E. coli ketopantoate reductase by mutagenesis and chemical rescue." Zheng R., Blanchard J.S. Biochemistry 39:16244-16251(2000) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF LYS-176 AND GLU-256, BIOPHYSICOCHEMICAL PROPERTIES.
[7]	"Biophysical tools to monitor enzyme-ligand interactions of enzymes involved in vitamin biosynthesis." Ciulli A., Abell C. Biochem. Soc. Trans. 33:767-771(2005) [PubMed] [Europe PMC] [Abstract] Cited for: LIGAND BINDING.
[8]	"Probing hot spots at protein-ligand binding sites: a fragment-based approach using biophysical methods." Ciulli A., Williams G., Smith A.G., Blundell T.L., Abell C. J. Med. Chem. 49:4992-5000(2006) [PubMed] [Europe PMC] [Abstract] Cited for: LIGAND BINDING, MUTAGENESIS OF ARG-31 AND ASN-98.
[9]	"Crystal structure of Escherichia coli ketopantoate reductase at 1.7 A resolution and insight into the enzyme mechanism." Matak-Vinkovic D., Vinkovic M., Saldanha S.A., Ashurst J.L., von Delft F., Inoue T., Miguel R.N., Smith A.G., Blundell T.L., Abell C. Biochemistry 40:14493-14500(2001) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS), PROTEIN SEQUENCE OF 1-9, MASS SPECTROMETRY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
[10]	"The crystal structure of Escherichia coli ketopantoate reductase with NADP+ bound." Lobley C.M.C., Ciulli A., Whitney H.M., Williams G., Smith A.G., Abell C., Blundell T.L. Biochemistry 44:8930-8939(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.09 ANGSTROMS) IN COMPLEX WITH NADP.
[11]	"pH-tuneable binding of 2'-phospho-ADP-ribose to ketopantoate reductase: a structural and calorimetric study." Ciulli A., Lobley C.M.C., Tuck K.L., Smith A.G., Blundell T.L., Abell C. Acta Crystallogr. D 63:171-178(2007) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH NADP ANALOG, MUTAGENESIS OF ASN-98; LYS-176 AND GLU-256.
[12]	"Crystal structure of Escherichia coli ketopantoate reductase in a ternary complex with NADP+ and pantoate bound: substrate recognition, conformational change, and cooperativity." Ciulli A., Chirgadze D.Y., Smith A.G., Blundell T.L., Abell C. J. Biol. Chem. 282:8487-8497(2007) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND NADP, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF LYS-72 AND SER-244.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U82664 Genomic DNA. Translation: AAB40181.1.
U00096 Genomic DNA. Translation: AAC73528.1.
AP009048 Genomic DNA. Translation: BAE76205.1.
U34923 Genomic DNA. Translation: AAA82703.1.

PIR

A64772.

RefSeq

NP_414959.1. NC_000913.2.
YP_488717.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1KS9	X-ray	1.70	A	1-291	[»]
1YJQ	X-ray	2.09	A	1-303	[»]
1YON	X-ray	1.95	A	1-303	[»]
2OFP	X-ray	2.30	A/B	1-303	[»]

ProteinModelPortal

P0A9J4.

SMR

P0A9J4. Positions 1-292.

ModBase

Search...

Protein-protein interaction databases

IntAct

P0A9J4. 4 interactions.

STRING

511145.b0425.

Proteomic databases

PRIDE

P0A9J4.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73528; AAC73528; b0425.
BAE76205; BAE76205; BAE76205.

GeneID

12933987.
945065.

KEGG

ecj:Y75_p0413.
eco:b0425.

PATRIC

32116001. VBIEscCol129921_0442.

Organism-specific databases

EchoBASE

EB3056.

EcoGene

EG13271. panE.

Phylogenomic databases

eggNOG

COG1893.

HOGENOM

HOG000050223.

KO

K00077.

OMA

IVCVKAY.

ProtClustDB

PRK06522.

Enzyme and pathway databases

BioCyc

EcoCyc:2-DEHYDROPANTOATE-REDUCT-MONOMER.
ECOL316407:JW0415-MONOMER.
MetaCyc:2-DEHYDROPANTOATE-REDUCT-MONOMER.

SABIO-RK

P0A9J4.

UniPathway

UPA00028; UER00004.

Gene expression databases

Genevestigator

P0A9J4.

Family and domain databases

Gene3D

1.10.1040.10. 1 hit.
3.40.50.720. 1 hit.

InterPro

IPR008927. 6-PGluconate_DH_C-like.
IPR003710. ApbA.
IPR013752. ApbA_C.
IPR013332. ApbA_N.
IPR013328. DH_multihelical.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

Pfam

PF02558. ApbA. 1 hit.
PF08546. ApbA_C. 1 hit.
[Graphical view]

SUPFAM

SSF48179. 6DGDH_C_like. 1 hit.

TIGRFAMs

TIGR00745. apbA_panE. 1 hit.

ProtoNet

Search...

Other

BindingDB

P0A9J4.

ChEMBL

CHEMBL4855.

EvolutionaryTrace

P0A9J4.

Entry information

Entry name

PANE_ECOLI

Accession

Primary (citable) accession number: P0A9J4
Secondary accession number(s): P77728, Q2MC01, Q46947

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 19, 2005
Last sequence update:	July 19, 2005
Last modified:	May 1, 2013
This is version 80 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program