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PDBsum entry 2rnt
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Hydrolase(endoribonuclease)
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PDB id
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2rnt
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References listed in PDB file
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Key reference
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Title
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Three-Dimensional structure of ribonuclease t1 complexed with guanylyl-2',5'-Guanosine at 1.8 a resolution.
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Authors
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J.Koepke,
M.Maslowska,
U.Heinemann,
W.Saenger.
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Ref.
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J Mol Biol, 1989,
206,
475-488.
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PubMed id
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Abstract
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The enzyme ribonuclease T1 (RNase T1) isolated from Aspergillus oryzae was
cocrystallized with the specific inhibitor guanylyl-2',5'-guanosine (2',5'-GpG)
and the structure refined by the stereochemically restrained least-squares
refinement method to a crystallographic R-factor of 14.9% for X-ray data above 3
sigma in the resolution range 6 to 1.8 A. The refined model consists of 781
protein atoms, 43 inhibitor atoms in a major site and 29 inhibitor atoms in a
minor site, 107 water oxygen atoms, and a metal site assigned as Ca. At the end
of the refinement, the orientation of His, Asn and Gln side-chains was
reinterpreted on the basis of two-dimensional nuclear magnetic resonance data.
The crystal packing and enzyme conformation of the RNase T1/2',5'-GpG complex
and of the near-isomorphous RNase T1/2'-GMP complex are comparable. The
root-mean-square deviation is 0.73 A between equivalent protein atoms.
Differences in the unit cell dimensions are mainly due to the bound inhibitor.
The 5'-terminal guanine of 2',5'-GpG binds to RNase T1 in much the same way as
in the 2'-GMP complex. In contrast, the hydrogen bonds between the catalytic
center and the phosphate group are different and the 3'-terminal guanine forms
no hydrogen bonds with the enzyme. This poor binding is reflected in a 2-fold
disorder of 2',5'-GpG (except the 5'-terminal guanine), which originates from
differences in the pucker of the 5'-terminal ribose. The pucker is C2'-exo for
the major site (2/3 occupancy) and C1'-endo for the minor site (1/3 occupancy).
The orientation of the major site is stabilized through stacking interactions
between the 3'-terminal guanine and His92, an amino acid necessary for
catalysis. This might explain the high inhibition rate observed for 2',5'-GpG,
which exceeds that of all other inhibitors of type 2',5'-GpN. On the basis of
distance criteria, one solvent peak in the electron density was identified as
metal ion, probably Ca2+. The ion is co-ordinated by the two Asp15 carboxylate
oxygen atoms and by six water molecules. The co-ordination polyhedron displays
approximate 4m2 symmetry.
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Secondary reference #1
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Title
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Crystal structure of guanosine-Free ribonuclease t1, Complexed with vanadate (v), Suggests conformational change upon substrate binding.
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Authors
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D.Kostrewa,
H.W.Choe,
U.Heinemann,
W.Saenger.
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Ref.
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Biochemistry, 1989,
28,
7592-7600.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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Three-Dimensional structure of the ribonuclease t1 2'-Gmp complex at 1.9-A resolution.
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Authors
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R.Arni,
U.Heinemann,
R.Tokuoka,
W.Saenger.
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Ref.
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J Biol Chem, 1988,
263,
15358-15368.
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PubMed id
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Secondary reference #3
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Title
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Struktur und funktion des enzyms ribonuclease t=1= (german)
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Authors
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R.Arni,
U.Heinemann,
W.Saenger.
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Ref.
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fresenius z anal chem, 1987,
327,
67.
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Secondary reference #4
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Title
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Restrained least-Squares refinement of the crystal structure of the ribonuclease t=1=(asterisk)2(prime)guanylic acid complex at 1.9 angstroms resolution
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Authors
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R.Arni,
U.Heinemann,
M.Maslowska,
R.Tokuoka,
W.Saenger.
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Ref.
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acta crystallogr ,sect b, 1987,
43,
549.
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Secondary reference #5
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Title
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Mechanism of guanosine recognition and RNA hydrolysis by ribonuclease t=1=
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Authors
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U.Heinemann,
W.Saenger.
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Ref.
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pure appl chem, 1985,
57,
417.
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Secondary reference #6
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Title
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The structural and sequence homology of a family of microbial ribonucleases
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Authors
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C.Hill,
G.Dodson,
U.Heinemann,
W.Saenger,
Y.Mitsui,
K.Nakamura,
S.Borisov,
G.Tischenko,
K.Polyakov,
S.Pavlovsky.
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Ref.
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trends biochem sci (pers, 1983,
8,
364.
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Secondary reference #7
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Title
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Ribonuclease t=1=. Mechanism of specific guanine recognition and RNA hydrolysis
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Authors
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U.Heinemann,
W.Saenger.
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Ref.
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jerusalem symp quantum chem, 1983,
16,
265.
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Secondary reference #8
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Title
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Crystallographic study of mechanism of ribonuclease t1-Catalysed specific RNA hydrolysis.
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Authors
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U.Heinemann,
W.Saenger.
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Ref.
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J Biomol Struct Dyn, 1983,
1,
523-538.
[DOI no: ]
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PubMed id
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Secondary reference #9
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Title
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Specific protein-Nucleic acid recognition in ribonuclease t1-2'-Guanylic acid complex: an x-Ray study.
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Authors
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U.Heinemann,
W.Saenger.
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Ref.
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Nature, 1982,
299,
27-31.
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PubMed id
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Secondary reference #10
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Title
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Crystallization of a complex between ribonuclease t1 and 2'-Guanylic acid.
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Authors
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U.Heinemann,
M.Wernitz,
A.Pähler,
W.Saenger,
G.Menke,
H.Rüterjans.
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Ref.
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Eur J Biochem, 1980,
109,
109-114.
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PubMed id
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