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PDBsum entry 9rnt
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Hydrolase(endoribonuclease)
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PDB id
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9rnt
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References listed in PDB file
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Key reference
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Title
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Ribonuclease t1 with free recognition and catalytic site: crystal structure analysis at 1.5 a resolution.
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Authors
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J.Martinez-Oyanedel,
H.W.Choe,
U.Heinemann,
W.Saenger.
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Ref.
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J Mol Biol, 1991,
222,
335-352.
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PubMed id
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Abstract
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The free form of ribonuclease T1 (RNase T1) has been crystallized at neutral pH,
and the three-dimensional structure of the enzyme has been determined at 1.5 A
nominal resolution. Restrained least-squares refinement yielded an R value of
14.3% for 12,623 structure amplitudes. The high resolution of the structure
analysis permits a detailed description of the solvent structure around RNase
T1, the reliable rotational setting of several side-chain amide and imidazole
groups and the identification of seven disordered residues. Among these, the
disordered and completely internal Val78 residue is noteworthy. In the RNase T1
crystal structures determined thus far it is always disordered in the absence of
bound guanosine, but not in its presence. A systematic analysis of hydrogen
bonding reveals the presence in RNase T1 of 40 three-center and an additional
seven four-center hydrogen bonds. Three-center hydrogen bonds occur
predominantly in the alpha-helix, where their minor components close 3(10)-type
turns, and in beta-sheets, where their minor components connect the peptide
nitrogen and carbonyl functions of the same residue. The structure of the free
form is compared with complexes of RNase T1 with filled base recognition site
and/or catalytic site. Several structural rearrangements occurring upon
inhibitor or substrate binding are clearly apparent. In conjunction with the
available biochemical knowledge, they are used to describe probable steps
occurring early during RNase T1-catalyzed phosphate transesterification.
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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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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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