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PDBsum entry 1b2m
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Hydrolase/RNA
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PDB id
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1b2m
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Contents |
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* Residue conservation analysis
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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 an isosteric phosphonate substrate analogue of gpu: alternate substrate binding modes and catalysis.
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Authors
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R.K.Arni,
L.Watanabe,
R.J.Ward,
R.J.Kreitman,
K.Kumar,
F.G.Walz.
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Ref.
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Biochemistry, 1999,
38,
2452-2461.
[DOI no: ]
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PubMed id
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Abstract
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The X-ray crystal structure of a complex between ribonuclease T1 and
guanylyl(3'-6')-6'-deoxyhomouridine (GpcU) has been determined at 2. 0 A
resolution. This ligand is an isosteric analogue of the minimal RNA substrate,
guanylyl(3'-5')uridine (GpU), where a methylene is substituted for the uridine
5'-oxygen atom. Two protein molecules are part of the asymmetric unit and both
have a GpcU bound at the active site in the same manner. The protein-protein
interface reveals an extended aromatic stack involving both guanines and three
enzyme phenolic groups. A third GpcU has its guanine moiety stacked on His92 at
the active site on enzyme molecule A and interacts with GpcU on molecule B in a
neighboring unit via hydrogen bonding between uridine ribose 2'- and 3'-OH
groups. None of the uridine moieties of the three GpcU molecules in the
asymmetric unit interacts directly with the protein. GpcU-active-site
interactions involve extensive hydrogen bonding of the guanine moiety at the
primary recognition site and of the guanosine 2'-hydroxyl group with His40 and
Glu58. On the other hand, the phosphonate group is weakly bound only by a single
hydrogen bond with Tyr38, unlike ligand phosphate groups of other substrate
analogues and 3'-GMP, which hydrogen-bonded with three additional active-site
residues. Hydrogen bonding of the guanylyl 2'-OH group and the phosphonate
moiety is essentially the same as that recently observed for a novel structure
of a RNase T1-3'-GMP complex obtained immediately after in situ hydrolysis of
exo-(Sp)-guanosine 2',3'-cyclophosphorothioate [Zegers et al. (1998) Nature
Struct. Biol. 5, 280-283]. It is likely that GpcU at the active site represents
a nonproductive binding mode for GpU [Steyaert, J., and Engleborghs (1995) Eur.
J. Biochem. 233, 140-144]. The results suggest that the active site of
ribonuclease T1 is adapted for optimal tight binding of both the guanylyl 2'-OH
and phosphate groups (of GpU) only in the transition state for catalytic
transesterification, which is stabilized by adjacent binding of the leaving
nucleoside (U) group.
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Secondary reference #1
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Title
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Three-Dimensional structure of gln25-Ribonuclease t1 at 1.84-A resolution: structural variations at the base recognition and catalytic sites.
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Authors
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R.K.Arni,
G.P.Pal,
K.G.Ravichandran,
A.Tulinsky,
F.G.Walz,
P.Metcalf.
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Ref.
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Biochemistry, 1992,
31,
3126-3135.
[DOI no: ]
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PubMed id
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Secondary reference #2
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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 #3
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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 #4
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Title
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Restrained least-Squares refinement of the crystal structure of the ribonuclease t1 2'-Guanylic acid complex at 1.9 angstroms resolution
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Authors
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R.Arni,
V.Heinemann,
M.Maslowska,
R.Tokuoka,
W.Saenger.
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Ref.
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acta crystallogr , sect b, 1987,
43,
548.
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Secondary reference #5
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Title
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Structure and function of the enzyme ribonuclease t1
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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 #6
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Title
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Crystallization of ribonuclease t1.
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Authors
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P.D.Martin,
A.Tulinsky,
F.G.Walz.
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Ref.
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J Mol Biol, 1980,
136,
95-97.
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PubMed id
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