Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.80 kDa 
• Atom Count: 971 
• Residue Count: 121 
• Unique protein chains: 2

2L0F

Solution NMR structure of human polymerase iota UBM2 (P692A mutant) in complex with ubiquitin

• DOI: 10.2210/pdb2L0F/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-07-01 Released: 2010-11-03 
• Deposition Author(s): Cui, G., Benirschke, R., Mer, G.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Structural Basis of Ubiquitin Recognition by Translesion Synthesis DNA Polymerase iota.

Cui, G., Benirschke, R.C., Tuan, H.F., Juranic, N., Macura, S., Botuyan, M.V., Mer, G.

(2010) Biochemistry 49: 10198-10207

• PubMed: 21049971 
• DOI: 10.1021/bi101303t
• Primary Citation of Related Structures:  
  2L0G, 2L0F, 2KTF


• PubMed Abstract: 
  

Cells have evolved mutagenic bypass mechanisms that prevent stalling of the replication machinery at DNA lesions. This process, translesion DNA synthesis (TLS), involves switching from high-fidelity DNA polymerases to specialized DNA polymerases that replicate through a variety of DNA lesions. In eukaryotes, polymerase switching during TLS is regulated by the DNA damage-triggered monoubiquitylation of PCNA. How the switch operates is unknown, but all TLS polymerases of the so-called Y-family possess PCNA and ubiquitin-binding domains that are important for their function. To gain insight into the structural mechanisms underlying the regulation of TLS by ubiquitylation, we have probed the interaction of ubiquitin with a conserved ubiquitin-binding motif (UBM2) of Y-family polymerase Polι. Using NMR spectroscopy, we have determined the structure of a complex of human Polι UBM2 and ubiquitin, revealing a novel ubiquitin recognition fold consisting of two α-helices separated by a central trans-proline residue conserved in all UBMs. We show that, different from the majority of ubiquitin complexes characterized to date, ubiquitin residue Ile44 only plays a modest role in the association of ubiquitin with Polι UBM2. Instead, binding of UBM2 is centered on the recognition of Leu8 in ubiquitin, which is essential for the interaction.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A	76	Homo sapiens	Mutation(s): 0  Gene Names: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC
Find proteins for P62979 (Homo sapiens) Explore P62979  Go to UniProtKB:  P62979
NIH Common Fund Data Resources
PHAROS:  P62979 GTEx:  ENSG00000143947

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase iota	B	45	Homo sapiens	Mutation(s): 1  Gene Names: POLI, RAD30B EC: 2.7.7.7
Find proteins for Q9UNA4 (Homo sapiens) Explore Q9UNA4  Go to UniProtKB:  Q9UNA4
NIH Common Fund Data Resources
PHAROS:  Q9UNA4 GTEx:  ENSG00000101751

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2L0F Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-07-01 
• Released Date: 2010-11-03 
Deposition Author(s): Cui, G., Benirschke, R., Mer, G.

Revision History 

• Version 1.0: 2010-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance