General Information

Database Accession: DI1000100

Name: C-terminal domain of human RPA32 complexed with UNG2

PDB ID: 1dpu PDB

Experimental method: NMR

Source organism: Homo sapiens

Proof of disorder: Inferred from motif

Primary publication of the structure:

Mer G, Bochkarev A, Gupta R, Bochkareva E, Frappier L, Ingles CJ, Edwards AM, Chazin WJ
Structural basis for the recognition of DNA repair proteins UNG2, XPA, and RAD52 by replication factor RPA.
(2000) Cell 103: 449-56

PMID: 11081631 PubMed

Abstract:

Replication protein A (RPA), the nuclear ssDNA-binding protein in eukaryotes, is essential to DNA replication, recombination, and repair. We have shown that a globular domain at the C terminus of subunit RPA32 contains a specific surface that interacts in a similar manner with the DNA repair enzyme UNG2 and repair factors XPA and RAD52, each of which functions in a different repair pathway. NMR structures of the RPA32 domain, free and in complex with the minimal interaction domain of UNG2, were determined, defining a common structural basis for linking RPA to the nucleotide excision, base excision, and recombinational pathways of repairing damaged DNA. Our findings support a hand-off model for the assembly and coordination of different components of the DNA repair machinery.

Function and Biology Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.

Molecular function:

damaged DNA binding Interacting selectively and non-covalently with damaged DNA. GeneOntology

enzyme binding Interacting selectively and non-covalently with any enzyme. GeneOntology

Biological process:

base-excision repair In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. GeneOntology

DNA recombination Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction. GeneOntology

positive regulation of cellular process Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GeneOntology

regulation of DNA recombination Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. GeneOntology

negative regulation of cellular process Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GeneOntology

Cellular component:

nucleoplasm That part of the nuclear content other than the chromosomes or the nucleolus. GeneOntology

Structure Summary Structural annotations of the participating protein chains.

Entry contents: 2 distinct polypeptide molecules

Chains: B, A

Notes: No modifications of the original PDB file.

Chain B

Name: Uracil-DNA glycosylase Disordered Inferred from motif

Source organism: Homo sapiens

Length: 16 residues

Sequence:Sequence according to PDB SEQRESRIQRNKAAALLRLAAR

UniProtKB AC: P13051 (positions: 73-88) UniProt Coverage: 5.1%

UniRef90 AC: UniRef90_P13051 (positions: 73-88) UniRef90

Chain A

Name: Replication protein A 32 kDa subunit Ordered

Source organism: Homo sapiens

Length: 99 residues

Sequence:Sequence according to PDB SEQRESANSQPSAGRAPISNPGMSEAGNFGGNSFMPANGLTVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIYSTVDDDHFKSTDAE

UniProtKB AC: P15927 (positions: 172-270) UniProt Coverage: 36.7%

UniRef90 AC: UniRef90_P15927 (positions: 172-270) UniRef90

Evidence Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding.

Chain B: Disordered Inferred from motif

The protein region involved in the interaction contains a known functional linear motif (LIG_RPA_C_Vert).

Chain A: Ordered

The RPA C-terminal domain involved in the interaction is known to adopt a stable structure in isolation (see Pfam domain PF08784). A solved monomeric structure of the domain is represented by PDB ID 4ou0.

Related Structure(s) Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap).

No related structure was found in the Protein Data Bank.

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