Structural analyses of peptide release factor 1 from Thermotoga maritima reveal domain flexibility required for its interaction with the ribosome

Dong Hae Shin; Jeroen Brandsen; Jaru Jancarik; Hisao Yokota; Rosalind Kim; Sung Hou Kim

doi:10.1016/j.jmb.2004.05.055

Structural analyses of peptide release factor 1 from Thermotoga maritima reveal domain flexibility required for its interaction with the ribosome

Dong Hae Shin, Jeroen Brandsen, Jaru Jancarik, Hisao Yokota, Rosalind Kim, Sung Hou Kim

Department of Pharmaceutical Sciences

Research output: Contribution to journal › Article › peer-review

72 Scopus citations

Abstract

We have determined the crystal structure of peptide chain release factor 1 (RF1) from Thermotoga maritima (gi 4981173) at 2.65Å resolution by selenomethionine single-wavelength anomalous dispersion (SAD) techniques. RF1 is a protein that recognizes stop codons and promotes the release of a nascent polypeptide from tRNA on the ribosome. Selenomethionine-labeled RF1 crystallized in space group P2₁ with three monomers per asymmetric unit. It has approximate dimensions of 75Å×70Å×45Å and is composed of four domains. The overall fold of each RF1 domain shows almost the same topology with Escherichia coli RF2, except that the RF1 N-terminal domain is shorter and the C-terminal domain is longer than that of RF2. The N-terminal domain of RF1 indicates a rigid-body movement relative to that of RF2 with an angle of ∼90°. Including these features, RF1 has a tripeptide anticodon PVT motif instead of the SPF motif of RF2, which confers the specificity towards the stop codons. The analyses of three molecules in the asymmetric unit and comparison with RF2 revealed the presence of dynamic movement of domains I and III, which are anchored to the central domain by hinge loops. The crystal structure of RF1 elucidates the intrinsic property of this family of having large domain movements for proper function with the ribosome.

Original language	English
Pages (from-to)	227-239
Number of pages	13
Journal	Journal of Molecular Biology
Volume	341
Issue number	1
DOIs	https://doi.org/10.1016/j.jmb.2004.05.055
State	Published - 30 Jul 2004

Bibliographical note

Funding Information:
We thank Dr Keith Henderson (Advanced Light Source, Lawrence Berkeley National Laboratory) for assistance during data collection. We are grateful to Dr Igor Grigoriev and Dr In-Geol Choi for target selection, Barbara Gold for cloning, Bruno A. Martinez and Marlene Henriquez for protein expression and cell growth. The work described here was supported by the National Institutes of Health (GM 62412).

Keywords

conformational change
crystal structure
DC, decoding center
gi 4981923
peptide release factor 1
PTC, peptidyl transferase center
RF, release factor
ribosome
SAD, single-wavelength anomalous dispersion

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10.1016/j.jmb.2004.05.055

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@article{c8e63c7a6a894f38b032817e1a5dba19,

title = "Structural analyses of peptide release factor 1 from Thermotoga maritima reveal domain flexibility required for its interaction with the ribosome",

abstract = "We have determined the crystal structure of peptide chain release factor 1 (RF1) from Thermotoga maritima (gi 4981173) at 2.65{\AA} resolution by selenomethionine single-wavelength anomalous dispersion (SAD) techniques. RF1 is a protein that recognizes stop codons and promotes the release of a nascent polypeptide from tRNA on the ribosome. Selenomethionine-labeled RF1 crystallized in space group P21 with three monomers per asymmetric unit. It has approximate dimensions of 75{\AA}×70{\AA}×45{\AA} and is composed of four domains. The overall fold of each RF1 domain shows almost the same topology with Escherichia coli RF2, except that the RF1 N-terminal domain is shorter and the C-terminal domain is longer than that of RF2. The N-terminal domain of RF1 indicates a rigid-body movement relative to that of RF2 with an angle of ∼90°. Including these features, RF1 has a tripeptide anticodon PVT motif instead of the SPF motif of RF2, which confers the specificity towards the stop codons. The analyses of three molecules in the asymmetric unit and comparison with RF2 revealed the presence of dynamic movement of domains I and III, which are anchored to the central domain by hinge loops. The crystal structure of RF1 elucidates the intrinsic property of this family of having large domain movements for proper function with the ribosome.",

keywords = "conformational change, crystal structure, DC, decoding center, gi 4981923, peptide release factor 1, PTC, peptidyl transferase center, RF, release factor, ribosome, SAD, single-wavelength anomalous dispersion",

author = "Shin, {Dong Hae} and Jeroen Brandsen and Jaru Jancarik and Hisao Yokota and Rosalind Kim and Kim, {Sung Hou}",

note = "Funding Information: We thank Dr Keith Henderson (Advanced Light Source, Lawrence Berkeley National Laboratory) for assistance during data collection. We are grateful to Dr Igor Grigoriev and Dr In-Geol Choi for target selection, Barbara Gold for cloning, Bruno A. Martinez and Marlene Henriquez for protein expression and cell growth. The work described here was supported by the National Institutes of Health (GM 62412).",

year = "2004",

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doi = "10.1016/j.jmb.2004.05.055",

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T1 - Structural analyses of peptide release factor 1 from Thermotoga maritima reveal domain flexibility required for its interaction with the ribosome

AU - Shin, Dong Hae

AU - Brandsen, Jeroen

AU - Jancarik, Jaru

AU - Yokota, Hisao

AU - Kim, Rosalind

AU - Kim, Sung Hou

N1 - Funding Information: We thank Dr Keith Henderson (Advanced Light Source, Lawrence Berkeley National Laboratory) for assistance during data collection. We are grateful to Dr Igor Grigoriev and Dr In-Geol Choi for target selection, Barbara Gold for cloning, Bruno A. Martinez and Marlene Henriquez for protein expression and cell growth. The work described here was supported by the National Institutes of Health (GM 62412).

PY - 2004/7/30

Y1 - 2004/7/30

N2 - We have determined the crystal structure of peptide chain release factor 1 (RF1) from Thermotoga maritima (gi 4981173) at 2.65Å resolution by selenomethionine single-wavelength anomalous dispersion (SAD) techniques. RF1 is a protein that recognizes stop codons and promotes the release of a nascent polypeptide from tRNA on the ribosome. Selenomethionine-labeled RF1 crystallized in space group P21 with three monomers per asymmetric unit. It has approximate dimensions of 75Å×70Å×45Å and is composed of four domains. The overall fold of each RF1 domain shows almost the same topology with Escherichia coli RF2, except that the RF1 N-terminal domain is shorter and the C-terminal domain is longer than that of RF2. The N-terminal domain of RF1 indicates a rigid-body movement relative to that of RF2 with an angle of ∼90°. Including these features, RF1 has a tripeptide anticodon PVT motif instead of the SPF motif of RF2, which confers the specificity towards the stop codons. The analyses of three molecules in the asymmetric unit and comparison with RF2 revealed the presence of dynamic movement of domains I and III, which are anchored to the central domain by hinge loops. The crystal structure of RF1 elucidates the intrinsic property of this family of having large domain movements for proper function with the ribosome.

AB - We have determined the crystal structure of peptide chain release factor 1 (RF1) from Thermotoga maritima (gi 4981173) at 2.65Å resolution by selenomethionine single-wavelength anomalous dispersion (SAD) techniques. RF1 is a protein that recognizes stop codons and promotes the release of a nascent polypeptide from tRNA on the ribosome. Selenomethionine-labeled RF1 crystallized in space group P21 with three monomers per asymmetric unit. It has approximate dimensions of 75Å×70Å×45Å and is composed of four domains. The overall fold of each RF1 domain shows almost the same topology with Escherichia coli RF2, except that the RF1 N-terminal domain is shorter and the C-terminal domain is longer than that of RF2. The N-terminal domain of RF1 indicates a rigid-body movement relative to that of RF2 with an angle of ∼90°. Including these features, RF1 has a tripeptide anticodon PVT motif instead of the SPF motif of RF2, which confers the specificity towards the stop codons. The analyses of three molecules in the asymmetric unit and comparison with RF2 revealed the presence of dynamic movement of domains I and III, which are anchored to the central domain by hinge loops. The crystal structure of RF1 elucidates the intrinsic property of this family of having large domain movements for proper function with the ribosome.

KW - conformational change

KW - crystal structure

KW - DC, decoding center

KW - gi 4981923

KW - peptide release factor 1

KW - PTC, peptidyl transferase center

KW - RF, release factor

KW - ribosome

KW - SAD, single-wavelength anomalous dispersion

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U2 - 10.1016/j.jmb.2004.05.055

DO - 10.1016/j.jmb.2004.05.055

M3 - Article

C2 - 15312775

AN - SCOPUS:4143064788

SN - 0022-2836

VL - 341

SP - 227

EP - 239

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

IS - 1

ER -

Structural analyses of peptide release factor 1 from Thermotoga maritima reveal domain flexibility required for its interaction with the ribosome

Abstract

Bibliographical note

Keywords

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