Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites

TY - JOUR

T1 - Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites

AU - Park, Sunghyouk

AU - Isaacson, Rivka

AU - Kim, Hyoung Tae

AU - Silver, Pamela A.

AU - Wagner, Gerhard

N1 - Funding Information: We acknowledge Mr. Gregory Heffron for assistance with the NMR experiments, Dr. Vladimir Gelev for the precursors to make ILV-methyl 13 C-prototonated samples, and Dr. Takuhiro Ito for excellent scientific communication. This research was supported by NIH (grants AI37581 and GM47467 to G.W., and grant GM36373 to P.A.S.). Maintenance of the instruments used for this research was in part supported by grant RR 00995. R.L.I. is a recipient of a Wellcome Prize Traveling Fellowship and gratefully acknowledges their support.

PY - 2005/7

Y1 - 2005/7

N2 - Ufd1 mediates ubiquitin fusion degradation by association with Npl4 and Cdc48/p97. The Ufd1-ubiquitin interaction is essential for transfer of substrates to the proteasome. However, the mechanism and specificity of ubiquitin recognition by Ufd1 are poorly understood due to the lack of detailed structural information. Here, we present the solution structure of yeast Ufd1 N domain and show that it has two distinct binding sites for mono- and polyubiquitin. The structure exhibits striking similarities to the Cdc48/p97 N domain. It contains the double-psi β barrel motif, which is thus identified as a ubiquitin binding domain. Significantly, Ufd1 shows higher affinity toward polyubiquitin than monoubiquitin, attributable to the utilization of separate binding sites with different affinities. Further studies revealed that the Ufd1-ubiquitin interaction involves hydrophobic contacts similar to those in well-characterized ubiquitin binding proteins. Our results provide a structural basis for a previously proposed synergistic binding of polyubiquitin by Cdc48/p97 and Ufd1.

AB - Ufd1 mediates ubiquitin fusion degradation by association with Npl4 and Cdc48/p97. The Ufd1-ubiquitin interaction is essential for transfer of substrates to the proteasome. However, the mechanism and specificity of ubiquitin recognition by Ufd1 are poorly understood due to the lack of detailed structural information. Here, we present the solution structure of yeast Ufd1 N domain and show that it has two distinct binding sites for mono- and polyubiquitin. The structure exhibits striking similarities to the Cdc48/p97 N domain. It contains the double-psi β barrel motif, which is thus identified as a ubiquitin binding domain. Significantly, Ufd1 shows higher affinity toward polyubiquitin than monoubiquitin, attributable to the utilization of separate binding sites with different affinities. Further studies revealed that the Ufd1-ubiquitin interaction involves hydrophobic contacts similar to those in well-characterized ubiquitin binding proteins. Our results provide a structural basis for a previously proposed synergistic binding of polyubiquitin by Cdc48/p97 and Ufd1.

UR - http://www.scopus.com/inward/record.url?scp=21744460209&partnerID=8YFLogxK

U2 - 10.1016/j.str.2005.04.013

DO - 10.1016/j.str.2005.04.013

M3 - Article

C2 - 16004872

AN - SCOPUS:21744460209

SN - 0969-2126

VL - 13

SP - 995

EP - 1005

JO - Structure

JF - Structure

IS - 7

ER -