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PDBsum entry 1a6f
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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 p protein structure: evolutionary origins in the translational apparatus.
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Authors
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T.Stams,
S.Niranjanakumari,
C.A.Fierke,
D.W.Christianson.
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Ref.
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Science, 1998,
280,
752-755.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of Bacillus subtilis ribonuclease P protein is reported at
2.6 angstroms resolution. This protein binds to ribonuclease P RNA to form a
ribonucleoprotein holoenzyme with optimal catalytic activity. Mutagenesis and
biochemical data indicate that an unusual left-handed betaalphabeta crossover
connection and a large central cleft in the protein form conserved RNA binding
sites; a metal binding loop may comprise a third RNA binding site. The unusual
topology is partly shared with ribosomal protein S5 and the ribosomal
translocase elongation factor G, which suggests evolution from a common RNA
binding ancestor in the primordial translational apparatus.
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Figure 2.
Fig. 2. Space-filling model of B. subtilis RNase P protein.
Site-directed mutagenesis studies with the E. coli C5 protein
(18) identify residues important for holoenzyme function
(yellow); B. subtilis numbering is used. Solvent-exposed
residues in the^ central cleft (Phe^16, Phe^20), on helix B (the
RNR motif: Arg60, Asn61, Lys64, Arg65), or on  strand 3
(Arg45) most likely contact RNA. Interestingly, the Arg45  His
substitution in C5 protein (B. subtilis numbering) results in a
temperature-sensitive phenotype defective in holoenzyme assembly
(18); correspondingly, this substitution must alter a critical
contact between the protein and RNA subunits. Substitution of^ a
buried residue (Phe^107, which appears as tryptophan in C5
protein) probably slightly perturbs the overall tertiary
structure, thereby compromising the overall complementarity of
protein and RNA subunits in the^ holoenzyme. Photocross-linking
studies with the B. subtilis holoenzyme^ (19) identify residues
on the protein subunit that contact the^ RNA subunit (green),
including residues at the NH[2]-terminus (Arg7) and helix C
(Arg108, Ser111) that flank helix B. These studies also
implicate Ser49 (red) and the central cleft for binding the 5
 leader
sequence^ of pre-tRNA^Asp in the holoenzyme-substrate complex.
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Figure 3.
Fig. 3. Ribbon plots (25) of the COOH-terminal domain of
ribosomal protein S5 (20) (PDB accession code 1PKP), RNase P
protein, and domain IV of the ribosomal translocase, EF-G (21)
(PDB accession code 1DAR). Left-handed  crossovers
are highlighted in yellow. Topological similarities suggest
evolutionary divergence from a primordial ribosomal ancestor.
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The above figures are
reprinted
by permission from the AAAs:
Science
(1998,
280,
752-755)
copyright 1998.
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