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PDBsum entry 1fus
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Hydrolase(endoribonuclease)
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PDB id
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1fus
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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 structures of ribonuclease f1 of fusarium moniliforme in its free form and in complex with 2'Gmp.
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Authors
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D.G.Vassylyev,
K.Katayanagi,
K.Ishikawa,
M.Tsujimoto-Hirano,
M.Danno,
A.Pähler,
O.Matsumoto,
M.Matsushima,
H.Yoshida,
K.Morikawa.
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Ref.
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J Mol Biol, 1993,
230,
979-996.
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PubMed id
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Abstract
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RNase F1, a guanine-specific ribonuclease from Fusarium moniliforme, was
crystallized in two different forms, in the absence of an inhibitor and in the
presence of 2'GMP. The crystal structure of the RNase F1 free form was solved by
the molecular replacement method, using the co-ordinates of the RNase T1 complex
with 2'GMP, and was refined to a final R-factor of 18.7%, using the data
extended to 1.3 A resolution. For the crystal structure of the RNase F1 complex
with 2'GMP, the solution of the molecular replacement method was obtained on the
basis of the co-ordinates of the RNase F1 free form, and was refined to a final
R-factor of 16.8%, using the data up to 2 A resolution. The two crystal
structures of the RNase F1 free form and the complex with 2'GMP are very similar
to each other as reflected by a small root-mean-square displacement (r.m.s.d.)
value of 0.43 A for all C alpha atoms. The main differences between the two
structures are associated with binding of 2'GMP in the substrate recognition
site in the loop between Tyr42 and Glu46. A structural comparison between RNase
F1 and RNase T1 shows a substantial similarity between all the C alpha atoms, as
evidenced by a r.m.s.d. value of 1.4 A. The loop from residues 32 to 38 was
strikingly different between these two enzymes, in both its conformation and its
hydrogen bonding schemes. The side-chain of a catalytically active residue,
His92, is shifted away from the catalytic site in RNase F1 by 1.3 A and 0.85 A
with respect to the corresponding positions in the RNase T1 free form and in the
RNase T1 complex with 2'GMP, respectively. In the RNase F1 complex, the guanine
base of 2'GMP has a syn conformation about the glycosyl bond, and the furanose
ring assumes a 3'-exo pucker, which is different from that found in the complex
with RNase T1. In the catalytic site of the RNase F1 complex with 2'GMP, one
water molecule was observed, which bridges the phosphate oxygen atoms of 2'GMP
and the side-chains of the catalytically important residues, His92 and Arg77,
through hydrogen bonds. A water molecule occupying the same position was found
in the RNase F1 free form. The significance of this water molecule in the
hydrolytic reaction is discussed.
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