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PDBsum entry 6rnt
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Hydrolase(endoribonuclease)
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PDB id
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6rnt
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References listed in PDB file
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Key reference
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Title
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Crystal structure of ribonuclease t1 complexed with adenosine 2'-Monophosphate at 1.8-A resolution.
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Authors
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J.Ding,
G.Koellner,
H.P.Grunert,
W.Saenger.
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Ref.
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J Biol Chem, 1991,
266,
15128-15134.
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PubMed id
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Abstract
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Ribonuclease T1 was purified from an Escherichia coli overproducing strain and
co-crystallized with adenosine 2'-monophosphate (2'-AMP) by microdialysis
against 50% (v/v) 2-methyl-2,4-pentanediol in 20 mM sodium acetate, 2 mM calcium
acetate, pH 4.2. The crystals have orthorhombic space group P2(1)2(1)2(1), with
cell dimensions a = 48.93(1), b = 46.57(4), c = 41.04(2) A; Z = 4 and V = 93520
A3. The crystal structure was determined on the basis of the isomorphous
structure of uncomplexed RNase T1 (Martinez-Oyanedel et al. (1991) submitted for
publication) and refined by least squares methods using stereochemical
restraints. The refinement was based on Fhkl of 7,445 reflections with Fo
greater than or equal to 1 sigma (Fo) in the resolution range of 10-1.8 A, and
converged at a crystallographic R factor of 0.149. The phosphate group of 2'-AMP
is tightly hydrogen-bonded to the side chains of the active site residues Tyr38,
His40, Glu58, Arg77, and His92, comparable with vanadate binding in the
respective complex (Kostrewa, D., Choe, H.-W., Heinemann, U., and Saenger, W.
(1989) Biochemistry 28, 7592-7600) and different from the complex with guanosine
2'-monophosphate (Arni, R., Heinemann, U., Tokuoka, R., and Saenger, W. (1988)
J. Biol. Chem. 263, 15358-15368) where the phosphate does not interact with
Arg77 and His92. The adenosine moiety is not located in the guanosine
recognition site but stacked on Gly74 carbonyl and His92 imidazole, which serve
as a subsite, as shown previously (Lenz, A., Cordes, F., Heinemann, U., and
Saenger, W. (1991) J. Biol. Chem. 266, 7661-7667); in addition, there are
hydrogen bonds adenine N6H . . . O Gly74 (minor component of three-center
hydrogen bond) and adenosine O5' . . . O delta Asn36. These binding interactions
readily explain why RNase T1 has some affinity for 2'-AMP. The molecular
structure of RNase T1 is only marginally affected by 2'-AMP binding. Its "empty"
guanosine-binding site features a flipped Asn43-Asn44 peptide bond and the side
chains of Tyr45, Glu46 adopt conformations typical for RNase T1 not involved in
guanosine binding. The side chains of amino acids Leu26, Ser35, Asp49, Val78 are
disordered. The disorder of Val78 is of interest since this amino acid is
located in a hydrophobic cavity, and the disorder appears to be correlated with
an "empty" guanosine-binding site. The two Asp15 carboxylate oxygens and six
water molecules coordinate a Ca2+ ion 8-fold in the form of a square antiprism.
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Secondary reference #1
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Title
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Crystal structure of the tyr45trp mutant of ribonuclease t1 in a complex with 2'-Adenylic acid.
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Authors
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G.Koellner,
H.P.Grunert,
O.Landt,
W.Saenger.
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Ref.
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Eur J Biochem, 1991,
201,
199-202.
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PubMed id
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