1og6

X-ray diffraction
2.8Å resolution

ydhF, an aldo-keto reductase from E.coli complexed with NADPH

Released:
Source organism: Escherichia coli K-12
Entry authors: Jeudy S, Abergel C, Claverie JM

Function and Biology Details

Reactions catalysed:
3 ATP = pppA2'p5'A2'p5'A + 2 diphosphate
Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine
D-galactose + O(2) = D-galacto-hexodialdose + H(2)O(2)
(1a) an (RNA) containing cytidine = an (RNA)-3'-cytidine-2',3'-cyclophosphate + a 5'-hydroxy-ribonucleotide-3'-(RNA)
dUTP + H(2)O = dUMP + diphosphate
Acts on substrates that are at least partially unfolded. The cleavage site P1 residue is normally between a pair of hydrophobic residues, such as Val-|-Val
Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate 
ATP + a protein = ADP + a phosphoprotein
(S)-2-hydroxy acid + O(2) = 2-oxo acid + H(2)O(2)
H(2) + A = AH(2)
1-deoxy-D-xylulose 5-phosphate + 2-iminoacetate + thiocarboxy-[sulfur-carrier protein ThiS] = 2-((2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate + [sulfur-carrier protein ThiS] + 2 H(2)O
GTP + H(2)O = GDP + phosphate
1-haloalkane + H(2)O = a primary alcohol + halide
Cleavage of peptide bonds with very broad specificity.
An aldehyde + NAD(P)(+) + H(2)O = a carboxylate + NAD(P)H
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
L-aspartate = D-aspartate
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
A long-chain aldehyde + O(2) + 2 NADPH = an alkane + formate + H(2)O + 2 NADP(+)
L-asparagine + H(2)O = L-aspartate + NH(3)
(1a) L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine
L-cystathionine + H(2)O = L-homocysteine + NH(3) + pyruvate
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein]
(1a) L-cystathionine = L-cysteine + 2-aminobut-2-enoate
Selective hydrolysis of -Xaa-Xaa-|-Yaa- bonds in which each of the Xaa can be either Arg or Lys and Yaa can be either Ser or Ala.
(1a) S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [HECT-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + S-ubiquitinyl-[HECT-type E3 ubiquitin transferase]-L-cysteine
(2S)-2-hydroxy-3,4-dioxopentyl phosphate = 3-hydroxy-2,4-dioxopentyl phosphate
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
ATP + phenylacetate + CoA = AMP + diphosphate + phenylacetyl-CoA
Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins
2 glutathione + ROOH = glutathione disulfide + H(2)O + ROH
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
TSAVLQ-|-SGFRK-NH(2) and SGVTFQ-|-GKFKK the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase are the two most reactive peptide substrates. The enzyme exhibits a strong preference for substrates containing Gln at P1 position and Leu at P2 position.
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|- and the P1' position is occupied by Gly-|-
Hydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose and cellotetraose, releasing cellobiose from the non-reducing ends of the chains
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
(S)-dihydroorotate + fumarate = orotate + succinate
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
(R)-10-hydroxystearate = oleate + H(2)O
NTP + H(2)O = NDP + phosphate
Maltose = alpha,alpha-trehalose
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
(3R)-3-hydroxyacyl-[acyl-carrier-protein] + NADP(+) = 3-oxoacyl-[acyl-carrier-protein] + NADPH
A beta-lactam + H(2)O = a substituted beta-amino acid
2 3-phospho-D-glycerate + 2 H(+) = D-ribulose 1,5-bisphosphate + CO(2) + H(2)O
RX + glutathione = HX + R-S-glutathione
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O
L-arginine + H(2)O = L-ornithine + urea
D-glyceraldehyde 3-phosphate = glycerone phosphate
S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
Myo-inositol phosphate + H(2)O = myo-inositol + phosphate
Cleaves -Ala-|-Ser- and -Ala-|-Ala- bonds in the scaffold protein.
L-fuculose 1-phosphate = glycerone phosphate + (S)-lactaldehyde
Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. Alpha-Casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec; and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs).
Autocatalytic release of the core protein from the N-terminus of the togavirus structural polyprotein by hydrolysis of a -Trp-|-Ser- bond.
Random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans, galactomannans and glucomannans
Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'.
Hydrolyzes glutaminyl bonds, and activity is further restricted by preferences for the amino acids in P6 - P1' that vary with the species of potyvirus, e.g. Glu-Xaa-Xaa-Tyr-Xaa-Gln-|-(Ser or Gly) for the enzyme from tobacco etch virus. The natural substrate is the viral polyprotein, but other proteins and oligopeptides containing the appropriate consensus sequence are also cleaved.
Hydrolyzes a Gly-|-Gly bond at its own C-terminus, commonly in the sequence -Tyr-Xaa-Val-Gly-|-Gly, in the processing of the potyviral polyprotein.
Autocatalytically cleaves itself from the polyprotein of the foot-and-mouth disease virus by hydrolysis of a Lys-|-Gly bond, but then cleaves host cell initiation factor eIF-4G at bonds -Gly-|-Arg- and -Lys-|-Arg-.
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
Maleate = fumarate
2 phenolic donor + H(2)O(2) = 2 phenoxyl radical of the donor + 2 H(2)O
Choline = trimethylamine + acetaldehyde
Acetyl-CoA + an alkane-alpha,omega-diamine = CoA + an N-acetyldiamine
5-methyltetrahydrofolate + NAD(P)(+) = 5,10-methylenetetrahydrofolate + NAD(P)H
2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
Hydrolysis of terminal (1->4)-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
ADP-alpha-D-glucose + D-glucose 6-phosphate = ADP + alpha,alpha-trehalose 6-phosphate
L-lysine = cadaverine + CO(2)
Eliminative cleavage of (1->4)-alpha-D-galacturonan to give oligosaccharides with 4-deoxy-alpha-D-galact-4-enuronosyl groups at their non-reducing ends
S-adenosyl-L-homocysteine + H(2)O = L-homocysteine + adenosine
Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
ATP + thymidine = ADP + thymidine 5'-phosphate
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
ATP + H(2)O = ADP + phosphate
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
ATP + AMP = 2 ADP
L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH
L-glutamate + H(2)O + NADP(+) = 2-oxoglutarate + NH(3) + NADPH
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(27) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(27)
NAD(P)H + a quinone = NAD(P)(+) + a hydroquinone
Beta-D-ribopyranose = beta-D-ribofuranose
ATP + pyridoxal = ADP + pyridoxal 5'-phosphate
Succinate + a quinone = fumarate + a quinol
Hydrolysis of --Pro-|- and to a lesser extent --Ala-|- in oligopeptides.
Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
Acetyl-CoA + L-serine = CoA + O-acetyl-L-serine
Pyridoxamine 5'-phosphate + H(2)O + O(2) = pyridoxal 5'-phosphate + NH(3) + H(2)O(2)
Release of an N-terminal amino acid, Xaa-|-Yaa-, in which Xaa is preferably Leu, but may be other amino acids including Pro although not Arg or Lys, and Yaa may be Pro. Amino acid amides and methyl esters are also readily hydrolyzed, but rates on arylamides are exceedingly low.
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
An N-acyl-L-homoserine lactone + H(2)O = an N-acyl-L-homoserine
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
N(6)-prenyladenine + acceptor + H(2)O = adenine + 3-methylbut-2-enal + reduced acceptor
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Release of an N-terminal amino acid, preferentially leucine, but not glutamic or aspartic acids.
Biochemical function:
Biological process:
  • not assigned
Cellular component:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Oxidoreductase YdhF Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 298 amino acids
Theoretical weight: 33.65 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P76187 (Residues: 1-298; Coverage: 100%)
Gene names: JW1639, b1647, ydhF
Sequence domains: Aldo/keto reductase family
Structure domains: NADP-dependent oxidoreductase domain

Ligands and Environments


Cofactor: Ligand NAP 3 x NAP
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: R3
Unit cell:
a: 174.529Å b: 174.529Å c: 97.923Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.207 0.207 0.238
Expression system: Escherichia coli BL21(DE3)