2or1

X-ray diffraction
2.5Å resolution

RECOGNITION OF A DNA OPERATOR BY THE REPRESSOR OF PHAGE 434. A VIEW AT HIGH RESOLUTION

Released:

Function and Biology Details

Reactions catalysed:
5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
An N-acyl-L-homoserine lactone + H(2)O = an N-acyl-L-homoserine
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'.
RX + glutathione = HX + R-S-glutathione
A phenyl acetate + H(2)O = a phenol + acetate
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate = (S)-allantoin + CO(2)
Reduced plastocyanin + oxidized ferredoxin + light = oxidized plastocyanin + reduced ferredoxin
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
dUTP + H(2)O = dUMP + diphosphate
(1a) NADP(+) = 2'-phospho-cyclic ADP-ribose + nicotinamide
ATP + AMP = 2 ADP
Cleaves -Ala-|-Ser- and -Ala-|-Ala- bonds in the scaffold protein.
(3R)-3-hydroxyacyl-[acyl-carrier-protein] + NADP(+) = 3-oxoacyl-[acyl-carrier-protein] + NADPH
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
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.
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.
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
ATP + thiamine = AMP + thiamine diphosphate
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
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
NAD(+) + glycine + sulfide = nicotinamide + ADP-5-ethyl-4-methylthiazole-2-carboxylate + 3 H(2)O
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
ATP + D-ribose = ADP + D-ribose 5-phosphate
ATP + RNA(n) = diphosphate + RNA(n+1)
S-adenosyl-L-methionine + [peptide chain release factor 1 or 2]-L-glutamine = S-adenosyl-L-homocysteine + [peptide chain release factor 1 or 2]-N(5)-methyl-L-glutamine
ATP + glycerol = ADP + sn-glycerol 3-phosphate
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.
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.
Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins
A beta-lactam + H(2)O = a substituted beta-amino acid
GDP-beta-L-fucose + NADP(+) = GDP-4-dehydro-alpha-D-rhamnose + NADPH
H(2) + A = AH(2)
Malonyl-CoA + an [acyl-carrier-protein] = CoA + a malonyl-[acyl-carrier-protein]
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
ATP + a protein = ADP + a phosphoprotein
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.
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O
ATP + H(2)O = ADP + phosphate
NTP + H(2)O = NDP + phosphate
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
Random hydrolysis of (1->6)-alpha-D-mannosidic linkages in unbranched (1->6)-mannans
Cleavage of peptide bonds with very broad specificity.
1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = ATP + 5-phospho-alpha-D-ribose 1-diphosphate
ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr)
ATP + L-glutamate + NH(3) = ADP + phosphate + L-glutamine
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
17-alpha-hydroxypregnenolone + [reduced NADPH--hemoprotein reductase] + O(2) = 3-beta-hydroxyandrost-5-en-17-one + acetate + [oxidized NADPH--hemoprotein reductase] + H(2)O
Palmitoyl-CoA + H(2)O = CoA + palmitate
(1a) NAD(+) = cyclic ADP-ribose + nicotinamide
A C(21)-steroid + [reduced NADPH--hemoprotein reductase] + O(2) = a 17-alpha-hydroxy-C(21)-steroid + [oxidized NADPH--hemoprotein reductase] + H(2)O
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
1-haloalkane + H(2)O = a primary alcohol + halide
5'-deoxyadenosine + H(2)O = 5-deoxy-D-ribose + adenine
2-lysophosphatidylcholine + H(2)O = glycerophosphocholine + a carboxylate
(S)-dihydroorotate + fumarate = orotate + succinate
L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate
Diphosphate + H(2)O = 2 phosphate
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
Peptidylproline (omega=180) = peptidylproline (omega=0)
5-hydroxyisourate + H(2)O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate
IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate
ATP + thymidine = ADP + thymidine 5'-phosphate
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
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.
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
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 + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro)
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
2 3-phospho-D-glycerate + 2 H(+) = D-ribulose 1,5-bisphosphate + CO(2) + H(2)O
Oleoyl-[acyl-carrier-protein] + H(2)O = [acyl-carrier-protein] + oleate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Repressor protein CI Chains: L, R
Molecule details ›
Chains: L, R
Length: 69 amino acids
Theoretical weight: 7.56 KDa
Source organism: Phage 434
UniProt:
  • Canonical: P16117 (Residues: 2-70; Coverage: 73%)
Gene name: CI
Sequence domains: Helix-turn-helix
Structure domains: lambda repressor-like DNA-binding domains
DNA (5'-D(*AP*AP*GP*TP*AP*CP*AP*AP*AP*CP*TP*TP*TP*CP*TP*TP*G P*TP*AP*T)-3') Chain: A
Molecule details ›
Chain: A
Length: 20 nucleotides
Theoretical weight: 6.11 KDa
Source organism: Phage 434
Expression system: Not provided
DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*GP*AP*AP*AP*GP*TP*TP*TP*GP*T P*AP*CP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 20 nucleotides
Theoretical weight: 6.16 KDa
Source organism: Phage 434
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: P212121
Unit cell:
a: 148.3Å b: 65Å c: 27.7Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 not available not available
Expression system: Not provided