6i59 | pdb_00006i59

Long wavelength native-SAD phasing of Sen1 helicase

Structural highlights

6i59 is a 1 chain structure with sequence from Baker's yeast. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	ADP, EDO, GOL, MG, PEG
Related:	5mzn
Gene:	SEN1, YLR430W, L9576.1 (Baker's yeast)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[SEN1_YEAST] ATP-dependent 5'->3' DNA/RNA helicase required for the expression and maturation of diverse classes of non-protein-coding RNAs like precursor tRNAs, rRNAs and small nuclear (snRNA) and nucleolar (snoRNA) RNAs. Directs RNA polymerase II transcription termination on snoRNAs as well as on several short protein-coding genes. May also play a role in transcription-coupled nucleotide excision repair.^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Publication Abstract from PubMed

Native single-wavelength anomalous dispersion (SAD) is an attractive experimental phasing technique as it exploits weak anomalous signals from intrinsic light scatterers (Z < 20). The anomalous signal of sulfur in particular, is enhanced at long wavelengths, however the absorption of diffracted X-rays owing to the crystal, the sample support and air affects the recorded intensities. Thereby, the optimal measurable anomalous signals primarily depend on the counterplay of the absorption and the anomalous scattering factor at a given X-ray wavelength. Here, the benefit of using a wavelength of 2.7 over 1.9 A is demonstrated for native-SAD phasing on a 266 kDa multiprotein-ligand tubulin complex (T2R-TTL) and is applied in the structure determination of an 86 kDa helicase Sen1 protein at beamline BL-1A of the KEK Photon Factory, Japan. Furthermore, X-ray absorption at long wavelengths was controlled by shaping a lysozyme crystal into spheres of defined thicknesses using a deep-UV laser, and a systematic comparison between wavelengths of 2.7 and 3.3 A is reported for native SAD. The potential of laser-shaping technology and other challenges for an optimized native-SAD experiment at wavelengths >3 A are discussed.

Long-wavelength native-SAD phasing: opportunities and challenges.,Basu S, Olieric V, Leonarski F, Matsugaki N, Kawano Y, Takashi T, Huang CY, Yamada Y, Vera L, Olieric N, Basquin J, Wojdyla JA, Bunk O, Diederichs K, Yamamoto M, Wang M IUCrJ. 2019 Apr 1;6(Pt 3):373-386. doi: 10.1107/S2052252519002756. eCollection, 2019 May 1. PMID:31098019^[7]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Steinmetz EJ, Conrad NK, Brow DA, Corden JL. RNA-binding protein Nrd1 directs poly(A)-independent 3'-end formation of RNA polymerase II transcripts. Nature. 2001 Sep 20;413(6853):327-31. PMID:11565036 doi:https://dx.doi.org/10.1038/35095090
↑ Ursic D, Chinchilla K, Finkel JS, Culbertson MR. Multiple protein/protein and protein/RNA interactions suggest roles for yeast DNA/RNA helicase Sen1p in transcription, transcription-coupled DNA repair and RNA processing. Nucleic Acids Res. 2004 Apr 30;32(8):2441-52. Print 2004. PMID:15121901 doi:https://dx.doi.org/10.1093/nar/gkh561
↑ Steinmetz EJ, Warren CL, Kuehner JN, Panbehi B, Ansari AZ, Brow DA. Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Mol Cell. 2006 Dec 8;24(5):735-46. PMID:17157256 doi:https://dx.doi.org/10.1016/j.molcel.2006.10.023
↑ Steinmetz EJ, Brow DA. Repression of gene expression by an exogenous sequence element acting in concert with a heterogeneous nuclear ribonucleoprotein-like protein, Nrd1, and the putative helicase Sen1. Mol Cell Biol. 1996 Dec;16(12):6993-7003. PMID:8943355
↑ Ursic D, Himmel KL, Gurley KA, Webb F, Culbertson MR. The yeast SEN1 gene is required for the processing of diverse RNA classes. Nucleic Acids Res. 1997 Dec 1;25(23):4778-85. PMID:9365256
↑ Rasmussen TP, Culbertson MR. The putative nucleic acid helicase Sen1p is required for formation and stability of termini and for maximal rates of synthesis and levels of accumulation of small nucleolar RNAs in Saccharomyces cerevisiae. Mol Cell Biol. 1998 Dec;18(12):6885-96. PMID:9819377
↑ Basu S, Olieric V, Leonarski F, Matsugaki N, Kawano Y, Takashi T, Huang CY, Yamada Y, Vera L, Olieric N, Basquin J, Wojdyla JA, Bunk O, Diederichs K, Yamamoto M, Wang M. Long-wavelength native-SAD phasing: opportunities and challenges. IUCrJ. 2019 Apr 1;6(Pt 3):373-386. doi: 10.1107/S2052252519002756. eCollection, 2019 May 1. PMID:31098019 doi:https://dx.doi.org/10.1107/S2052252519002756

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[1] Steinmetz EJ, Conrad NK, Brow DA, Corden JL. RNA-binding protein Nrd1 directs poly(A)-independent 3'-end formation of RNA polymerase II transcripts. Nature. 2001 Sep 20;413(6853):327-31. PMID:11565036 doi:https://dx.doi.org/10.1038/35095090

[2] Ursic D, Chinchilla K, Finkel JS, Culbertson MR. Multiple protein/protein and protein/RNA interactions suggest roles for yeast DNA/RNA helicase Sen1p in transcription, transcription-coupled DNA repair and RNA processing. Nucleic Acids Res. 2004 Apr 30;32(8):2441-52. Print 2004. PMID:15121901 doi:https://dx.doi.org/10.1093/nar/gkh561

[3] Steinmetz EJ, Warren CL, Kuehner JN, Panbehi B, Ansari AZ, Brow DA. Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Mol Cell. 2006 Dec 8;24(5):735-46. PMID:17157256 doi:https://dx.doi.org/10.1016/j.molcel.2006.10.023

[4] Steinmetz EJ, Brow DA. Repression of gene expression by an exogenous sequence element acting in concert with a heterogeneous nuclear ribonucleoprotein-like protein, Nrd1, and the putative helicase Sen1. Mol Cell Biol. 1996 Dec;16(12):6993-7003. PMID:8943355

[5] Ursic D, Himmel KL, Gurley KA, Webb F, Culbertson MR. The yeast SEN1 gene is required for the processing of diverse RNA classes. Nucleic Acids Res. 1997 Dec 1;25(23):4778-85. PMID:9365256

[6] Rasmussen TP, Culbertson MR. The putative nucleic acid helicase Sen1p is required for formation and stability of termini and for maximal rates of synthesis and levels of accumulation of small nucleolar RNAs in Saccharomyces cerevisiae. Mol Cell Biol. 1998 Dec;18(12):6885-96. PMID:9819377

[7] Basu S, Olieric V, Leonarski F, Matsugaki N, Kawano Y, Takashi T, Huang CY, Yamada Y, Vera L, Olieric N, Basquin J, Wojdyla JA, Bunk O, Diederichs K, Yamamoto M, Wang M. Long-wavelength native-SAD phasing: opportunities and challenges. IUCrJ. 2019 Apr 1;6(Pt 3):373-386. doi: 10.1107/S2052252519002756. eCollection, 2019 May 1. PMID:31098019 doi:https://dx.doi.org/10.1107/S2052252519002756

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6i59 | pdb_00006i59

Long wavelength native-SAD phasing of Sen1 helicase

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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