4xk2

X-ray diffraction
1.9Å resolution

Crystal structure of aldo-keto reductase from Polaromonas sp. JS666

Released:
Source organism: Polaromonas sp. JS666
Entry authors: Gasiorowska OA, Handing KB, Shabalin IG, Sroka P, Hillerich BS, Bonanno J, Seidel R, Almo SC, Minor W, New York Structural Genomics Research Consortium (NYSGRC)

Function and Biology Details

Reactions catalysed:
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)
IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate
dUTP + H(2)O = dUMP + diphosphate
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
1-(5-phospho-beta-D-ribosyl)-5-((5-phospho-beta-D-ribosylamino)methylideneamino)imidazole-4-carboxamide = 5-((5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino)-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide
2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP
5-phospho-beta-D-ribosylamine + diphosphate + L-glutamate = L-glutamine + 5-phospho-alpha-D-ribose 1-diphosphate + H(2)O
ATP + a protein = ADP + a phosphoprotein
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
N-(5-phospho-D-ribosyl)-anthranilate + diphosphate = anthranilate + 5-phospho-alpha-D-ribose 1-diphosphate
S-adenosyl-L-methionine + pseudouridine(1915) in 23S rRNA = S-adenosyl-L-homocysteine + N(3)-methylpseudouridine(1915) in 23S rRNA
GTP = 3',5'-cyclic GMP + diphosphate
(1a) [acetyl-CoA C-acyltransferase]-S-acyl-L-cyteine + acetyl-CoA = 3-oxoacyl-CoA + [acetyl-CoA C-acyltransferase]-L-cyteine
ATP-dependent breakage, passage and rejoining of double-stranded DNA
(R)-propane-1,2-diol + NAD(+) = (R)-lactaldehyde + NADH
2 alpha,alpha'-trehalose 6-mycolate = alpha,alpha'-trehalose + alpha,alpha'-trehalose 6,6'-bismycolate
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.
GTP + H(2)O = GDP + phosphate
4-amino-2-methyl-5-diphosphomethylpyrimidine + 2-((2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate = diphosphate + thiamine phosphate + CO(2)
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
Cleavage of peptide bonds with very broad specificity.
ATP-dependent cleavage of peptide bonds with broad specificity.
N(2)-acetyl-L-ornithine + L-glutamate = L-ornithine + N-acetyl-L-glutamate
2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
Diphosphate + H(2)O = 2 phosphate
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)
Chorismate = prephenate
L-asparagine + H(2)O = L-aspartate + NH(3)
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein]
2 L-tyrosyl-tRNA(Tyr) = 2 tRNA(Tyr) + cyclo(L-tyrosyl-L-tyrosyl)
L-alanine = D-alanine
D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N(6)-acetyl-L-lysine
Acetyl-CoA + alpha-D-glucosamine 1-phosphate = CoA + N-acetyl-alpha-D-glucosamine 1-phosphate
CoA-(4'-phosphopantetheine) + apo-[acyl-carrier-protein] = adenosine 3',5'-bisphosphate + holo-[acyl-carrier-protein]
Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins
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
Protein N(6)-(dihydrolipoyl)lysine + NAD(+) = protein N(6)-(lipoyl)lysine + NADH
Cyclo(L-tyrosyl-L-tyrosyl) + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H(+) + O(2) = mycocyclosin + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H(2)O
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
ATP + shikimate = ADP + shikimate 3-phosphate
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.
Tuberculosinyl diphosphate + adenosine = 1-tuberculosinyladenosine + diphosphate
Geranyl diphosphate + isopentenyl diphosphate = diphosphate + (2Z,6E)-farnesyl diphosphate
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
Isochorismate = salicylate + pyruvate
ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate + meso-2,6-diaminoheptanedioate = ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminoheptanedioate
NTP + H(2)O = NDP + phosphate
dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-beta-L-rhamnose
Cleaves proteins of the adenovirus and its host cell at two consensus sites: -Yaa-Xaa-Gly-Gly-|-Xaa- and -Yaa-Xaa-Gly-Xaa-|-Gly- (in which Yaa is Met, Ile or Leu, and Xaa is any amino acid).
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
ATP + pyruvate = ADP + phosphoenolpyruvate
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
UTP + N-acetyl-alpha-D-glucosamine 1-phosphate = diphosphate + UDP-N-acetyl-alpha-D-glucosamine
N-(5-phospho-beta-D-ribosyl)anthranilate = 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate
5,10-methylenetetrahydrofolate + dUMP + NADPH = dTMP + tetrahydrofolate + NADP(+)
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.
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
ATP = 3',5'-cyclic AMP + diphosphate
D-glyceraldehyde 3-phosphate = glycerone phosphate
Cleaves -Ala-|-Ser- and -Ala-|-Ala- bonds in the scaffold protein.
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).
(1a) [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate = [enzyme]-N(tau)-phospho-L-histidine + 2/3-phospho-D-glycerate
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.
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
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'.
Trans,octacis-decaprenylphospho-beta-D-ribofuranose + FAD = trans,octacis-decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose + FADH(2)
L-lysine + 2-oxoglutarate = (S)-2-amino-6-oxohexanoate + L-glutamate
Androstan-3-alpha,17-beta-diol + NAD(+) = 17-beta-hydroxyandrostan-3-one + NADH
Peptidylproline (omega=180) = peptidylproline (omega=0)
5-methyltetrahydrofolate + NAD(P)(+) = 5,10-methylenetetrahydrofolate + NAD(P)H
S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleotide)-[mRNA]
ATP + succinate + CoA = ADP + phosphate + succinyl-CoA
[a protein]-serine/threonine phosphate + H(2)O = [a protein]-serine/threonine + phosphate
Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units
D-fructose 1,6-bisphosphate + H(2)O = D-fructose 6-phosphate + phosphate
ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate
(S)-malate = fumarate + H(2)O
Succinate semialdehyde + NAD(P)(+) + H(2)O = succinate + NAD(P)H
L-quinate + NAD(P)(+) = 3-dehydroquinate + NAD(P)H
ADP-alpha-D-glucose + D-glucose 6-phosphate = ADP + alpha,alpha-trehalose 6-phosphate
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).
Acetyl-CoA + H(2)O + glyoxylate = (S)-malate + CoA
Chorismate = isochorismate
ATP + protoporphyrin IX + Mg(2+) + H(2)O = ADP + phosphate + Mg-protoporphyrin IX + 2 H(+)
Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
Acyl-CoA + 1,2-diacylglycerol = CoA + triacylglycerol
S-formylglutathione + H(2)O = glutathione + formate
S-adenosyl-L-methionine + uracil(1498) in 16S rRNA = S-adenosyl-L-homocysteine + N(3)-methyluracil(1498) in 16S rRNA 
ATP + dTMP = ADP + dTDP
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
An ultra-long-chain mono-unsaturated acyl-[acyl-carrier protein] + a malonyl-[acyl-carrier protein] = an ultra-long-chain mono-unsaturated 3-oxo-fatty acyl-[acyl-carrier protein] + CO(2) + a holo-[acyl-carrier protein]
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
Nucleoside 3',5'-cyclic phosphate + H(2)O = nucleoside 5'-phosphate
Nucleoside 2',3'-cyclic phosphate + H(2)O = nucleoside 3'-phosphate
Beta-D-ribopyranose = beta-D-ribofuranose
ATP + glycerol = ADP + sn-glycerol 3-phosphate
Succinate + a quinone = fumarate + a quinol
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.
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H(2)O
O-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate
Pyridoxamine 5'-phosphate + H(2)O + O(2) = pyridoxal 5'-phosphate + NH(3) + H(2)O(2)
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
AMP + H(2)O = D-ribose 5-phosphate + adenine
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
Hydrolysis of terminal, non-reducing (1->4)-linked alpha-D-glucose residues with release of alpha-D-glucose
Hydrolysis of terminal, non-reducing beta-D-mannose residues in beta-D-mannosides
Acetyl-CoA + malonyl-[acyl-carrier-protein] = acetoacetyl-[acyl-carrier-protein] + CoA + CO(2) 
ATP + H(2)O = ADP + phosphate
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + NADPH
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
Release of an N-terminal amino acid, preferentially leucine, but not glutamic or aspartic acids.
ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA
ATP + propanoyl-CoA + HCO(3)(-) = ADP + phosphate + (S)-methylmalonyl-CoA
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo octamer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Aldo_ket_red domain-containing protein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 344 amino acids
Theoretical weight: 37.41 KDa
Source organism: Polaromonas sp. JS666
Expression system: Escherichia coli
UniProt:
  • Canonical: Q124A1 (Residues: 1-343; Coverage: 100%)
Gene name: Bpro_4249
Sequence domains: Aldo/keto reductase family
Structure domains: NADP-dependent oxidoreductase domain

Ligands and Environments

2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: I422
Unit cell:
a: 105.11Å b: 105.11Å c: 479.569Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.162 0.16 0.185
Expression system: Escherichia coli