2gwf: Difference between revisions
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[[Image:2gwf.gif|left|200px]] | [[Image:2gwf.gif|left|200px]] | ||
'''Structure of a USP8-NRDP1 complex''' | {{Structure | ||
|PDB= 2gwf |SIZE=350|CAPTION= <scene name='initialview01'>2gwf</scene>, resolution 2.30Å | |||
|SITE= | |||
|LIGAND= | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/Ubiquitin_thiolesterase Ubiquitin thiolesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.2.15 3.1.2.15] | |||
|GENE= USP8, KIAA0055, UBPY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), RNF41 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | |||
}} | |||
'''Structure of a USP8-NRDP1 complex''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2GWF is a [ | 2GWF is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GWF OCA]. | ||
==Reference== | ==Reference== | ||
Amino-terminal dimerization, NRDP1-rhodanese interaction, and inhibited catalytic domain conformation of the ubiquitin-specific protease 8 (USP8)., Avvakumov GV, Walker JR, Xue S, Finerty PJ Jr, Mackenzie F, Newman EM, Dhe-Paganon S, J Biol Chem. 2006 Dec 8;281(49):38061-70. Epub 2006 Oct 11. PMID:[http:// | Amino-terminal dimerization, NRDP1-rhodanese interaction, and inhibited catalytic domain conformation of the ubiquitin-specific protease 8 (USP8)., Avvakumov GV, Walker JR, Xue S, Finerty PJ Jr, Mackenzie F, Newman EM, Dhe-Paganon S, J Biol Chem. 2006 Dec 8;281(49):38061-70. Epub 2006 Oct 11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17035239 17035239] | ||
[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
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[[Category: protein-protein complex]] | [[Category: protein-protein complex]] | ||
[[Category: sgc]] | [[Category: sgc]] | ||
[[Category: structural | [[Category: structural genomic]] | ||
[[Category: structural genomics consortium]] | [[Category: structural genomics consortium]] | ||
[[Category: ubl conjugation pathway]] | [[Category: ubl conjugation pathway]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:09:59 2008'' | ||
Revision as of 15:10, 20 March 2008
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| 2gwf, resolution 2.30Å | |||||||||||||
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| Gene: | USP8, KIAA0055, UBPY (Homo sapiens), RNF41 (Homo sapiens) | ||||||||||||
| Activity: | Ubiquitin thiolesterase, with EC number 3.1.2.15 | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
Structure of a USP8-NRDP1 complex
Overview
Ubiquitin-specific protease 8 (USP8) hydrolyzes mono and polyubiquitylated targets such as epidermal growth factor receptors and is involved in clathrin-mediated internalization. In 1182 residues, USP8 contains multiple domains, including coiled-coil, rhodanese, and catalytic domains. We report the first high-resolution crystal structures of these domains and discuss their implications for USP8 function. The amino-terminal domain is a homodimer with a novel fold. It is composed of two five-helix bundles, where the first helices are swapped, and carboxyl-terminal helices are extended in an antiparallel fashion. The structure of the rhodanese domain, determined in complex with the E3 ligase NRDP1, reveals the canonical rhodanese fold but with a distorted primordial active site. The USP8 recognition domain of NRDP1 has a novel protein fold that interacts with a conserved peptide loop of the rhodanese domain. A consensus sequence of this loop is found in other NRDP1 targets, suggesting a common mode of interaction. The structure of the carboxyl-terminal catalytic domain of USP8 exhibits the conserved tripartite architecture but shows unique traits. Notably, the active site, including the ubiquitin binding pocket, is in a closed conformation, incompatible with substrate binding. The presence of a zinc ribbon subdomain near the ubiquitin binding site further suggests a polyubiquitin-specific binding site and a mechanism for substrate induced conformational changes.
About this Structure
2GWF is a Protein complex structure of sequences from Homo sapiens. Full crystallographic information is available from OCA.
Reference
Amino-terminal dimerization, NRDP1-rhodanese interaction, and inhibited catalytic domain conformation of the ubiquitin-specific protease 8 (USP8)., Avvakumov GV, Walker JR, Xue S, Finerty PJ Jr, Mackenzie F, Newman EM, Dhe-Paganon S, J Biol Chem. 2006 Dec 8;281(49):38061-70. Epub 2006 Oct 11. PMID:17035239
Page seeded by OCA on Thu Mar 20 17:09:59 2008
Proteopedia Page Contributors and Editors (what is this?)
- Pages with broken file links
- Homo sapiens
- Protein complex
- Ubiquitin thiolesterase
- Arrowsmith, C H.
- Avvakumov, G V.
- Bochkarev, A.
- Butler-Cole, C.
- Dhe-Paganon, S.
- Edwards, A M.
- Jr., P J.Finerty.
- Newman, E M.
- SGC, Structural Genomics Consortium.
- Sundstrom, M.
- Walker, J R.
- Weigelt, J.
- Xue, S.
- E3 ligase
- Hydrolase
- Protease
- Protein ubiquitination
- Protein-protein complex
- Sgc
- Structural genomic
- Structural genomics consortium
- Ubl conjugation pathway
