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Solution structure and Rpn1 interaction of the UBL domain of human RNA polymerase II C-terminal domain phosphatase.

Yun JH, Ko S, Lee CK, Cheong HK, Cheong C, Yoon JB, Lee W - PLoS ONE (2013)

Bottom Line: The UBL domain of hUBLCP1 has a unique β-strand (β3) and β3-α2 loop, instead of the canonical β4 observed in other UBL domains.The molecular topology and secondary structures are different from those of known UBL domains including that of fly UBLCP1.The positively charged residues of the β3-α2 loop are involved in interacting with the C-terminal leucine-rich repeat-like domain of Rpn1.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.

ABSTRACT
The ubiquitin-like modifier (UBL) domain of ubiquitin-like domain proteins (UDPs) interacts specifically with subunits of the 26 S proteasome. A novel UDP, ubiquitin-like domain-containing C-terminal domain phosphatase (UBLCP1), has been identified as an interacting partner of the 26 S proteasome. We determined the high-resolution solution structure of the UBL domain of human UBLCP1 by nuclear magnetic resonance spectroscopy. The UBL domain of hUBLCP1 has a unique β-strand (β3) and β3-α2 loop, instead of the canonical β4 observed in other UBL domains. The molecular topology and secondary structures are different from those of known UBL domains including that of fly UBLCP1. Data from backbone dynamics shows that the β3-α2 loop is relatively rigid although it might have intrinsic dynamic profile. The positively charged residues of the β3-α2 loop are involved in interacting with the C-terminal leucine-rich repeat-like domain of Rpn1.

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Related in: MedlinePlus

Resonance assignment and solution structure of the UBL domain of hUBLCP1.(A) 1H-15N HSQC spectrum for the UBL domain was obtained using a Bruker DRX 900 MHz equipped with a cryoprobe. All backbone resonances in HSQC spectrum are labeled. (B) Molecular topology shows that the UBL domain of hUBLCP1 is composed of four β-strands and two α-helices. The unique β3-α2 loop exists in the same location in which β4 is usually found in the other UBLs. (C) The 20 lowest-energy structures were superimposed and fitted for the restraint energy minimization (REM) average structure using backbone atoms, Cα, N, and CO and the MOLMOL program. (D) Ribbon diagram shows molecular topology of the UBL domain generated by the Pymol program. The four β-strands and two α-helices are labeled on the structure.
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pone-0062981-g001: Resonance assignment and solution structure of the UBL domain of hUBLCP1.(A) 1H-15N HSQC spectrum for the UBL domain was obtained using a Bruker DRX 900 MHz equipped with a cryoprobe. All backbone resonances in HSQC spectrum are labeled. (B) Molecular topology shows that the UBL domain of hUBLCP1 is composed of four β-strands and two α-helices. The unique β3-α2 loop exists in the same location in which β4 is usually found in the other UBLs. (C) The 20 lowest-energy structures were superimposed and fitted for the restraint energy minimization (REM) average structure using backbone atoms, Cα, N, and CO and the MOLMOL program. (D) Ribbon diagram shows molecular topology of the UBL domain generated by the Pymol program. The four β-strands and two α-helices are labeled on the structure.

Mentions: All backbone resonance assignments were completed with data from HNCA, CBCACONH, and HNCACB experiments (Fig. 1A). Most of the side chain assignments were made based on 3D HCCH-TOCSY and 15N-edited TOCSY-HSQC experiments. Secondary structures were determined from the chemical shift indices (CSIs), NOEs, and 3JHNα coupling constant values.


Solution structure and Rpn1 interaction of the UBL domain of human RNA polymerase II C-terminal domain phosphatase.

Yun JH, Ko S, Lee CK, Cheong HK, Cheong C, Yoon JB, Lee W - PLoS ONE (2013)

Resonance assignment and solution structure of the UBL domain of hUBLCP1.(A) 1H-15N HSQC spectrum for the UBL domain was obtained using a Bruker DRX 900 MHz equipped with a cryoprobe. All backbone resonances in HSQC spectrum are labeled. (B) Molecular topology shows that the UBL domain of hUBLCP1 is composed of four β-strands and two α-helices. The unique β3-α2 loop exists in the same location in which β4 is usually found in the other UBLs. (C) The 20 lowest-energy structures were superimposed and fitted for the restraint energy minimization (REM) average structure using backbone atoms, Cα, N, and CO and the MOLMOL program. (D) Ribbon diagram shows molecular topology of the UBL domain generated by the Pymol program. The four β-strands and two α-helices are labeled on the structure.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3646893&req=5

pone-0062981-g001: Resonance assignment and solution structure of the UBL domain of hUBLCP1.(A) 1H-15N HSQC spectrum for the UBL domain was obtained using a Bruker DRX 900 MHz equipped with a cryoprobe. All backbone resonances in HSQC spectrum are labeled. (B) Molecular topology shows that the UBL domain of hUBLCP1 is composed of four β-strands and two α-helices. The unique β3-α2 loop exists in the same location in which β4 is usually found in the other UBLs. (C) The 20 lowest-energy structures were superimposed and fitted for the restraint energy minimization (REM) average structure using backbone atoms, Cα, N, and CO and the MOLMOL program. (D) Ribbon diagram shows molecular topology of the UBL domain generated by the Pymol program. The four β-strands and two α-helices are labeled on the structure.
Mentions: All backbone resonance assignments were completed with data from HNCA, CBCACONH, and HNCACB experiments (Fig. 1A). Most of the side chain assignments were made based on 3D HCCH-TOCSY and 15N-edited TOCSY-HSQC experiments. Secondary structures were determined from the chemical shift indices (CSIs), NOEs, and 3JHNα coupling constant values.

Bottom Line: The UBL domain of hUBLCP1 has a unique β-strand (β3) and β3-α2 loop, instead of the canonical β4 observed in other UBL domains.The molecular topology and secondary structures are different from those of known UBL domains including that of fly UBLCP1.The positively charged residues of the β3-α2 loop are involved in interacting with the C-terminal leucine-rich repeat-like domain of Rpn1.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.

ABSTRACT
The ubiquitin-like modifier (UBL) domain of ubiquitin-like domain proteins (UDPs) interacts specifically with subunits of the 26 S proteasome. A novel UDP, ubiquitin-like domain-containing C-terminal domain phosphatase (UBLCP1), has been identified as an interacting partner of the 26 S proteasome. We determined the high-resolution solution structure of the UBL domain of human UBLCP1 by nuclear magnetic resonance spectroscopy. The UBL domain of hUBLCP1 has a unique β-strand (β3) and β3-α2 loop, instead of the canonical β4 observed in other UBL domains. The molecular topology and secondary structures are different from those of known UBL domains including that of fly UBLCP1. Data from backbone dynamics shows that the β3-α2 loop is relatively rigid although it might have intrinsic dynamic profile. The positively charged residues of the β3-α2 loop are involved in interacting with the C-terminal leucine-rich repeat-like domain of Rpn1.

Show MeSH
Related in: MedlinePlus