General Information

Database accession: MF2120007

Name: UmuD' protein filament

PDB ID: 1ay9 PDB

Experimental method: X-ray (3.00 Å)

Assembly: homodimer

Source organism: Escherichia coli O157:H7

Primer publication of the structure:

Peat TS, Frank EG, McDonald JP, Levine AS, Woodgate R, Hendrickson WA
The UmuD' protein filament and its potential role in damage induced mutagenesis.
(1996) Structure 4: 1401-12

PMID: 8994967 PubMed

Abstract:

CONCLUSIONS: The activation of UmuD to UmuD' appears to cause a large conformational change in the protein which allows it to form oligomers in solution at physiologically relevant concentrations. Properties of these oligomers are consistent with the filament structures seen in crystals of UmuD'.
RESULTS: Recent X-ray crystallographic analysis shows that in addition to forming molecular dimers, the N- and C-terminal tails of UmuD' extend from a globular beta structure to associate and produce crystallized filaments. We have investigated this phenomenon and find that these filaments appear to relate to biological activity. Higher order oligomers are found in solution with UmuD', but not with UmuD nor with a mutant of UmuD' lacking the extended N terminus. Deletion of the N terminus of UmuD' does not affect its ability to form molecular dimers but does severely compromise its ability to interact with a RecA-DNA filament and to participate in mutagenesis. Mutations in the C terminus of UmuD' result in both gain and loss of function for mutagenesis.
BACKGROUND: Damage induced 'SOS mutagenesis' may occur transiently as part of the global SOS response to DNA damage in bacteria. A key participant in this process is the UmuD protein, which is produced in an inactive from but converted to the active form, UmuD', by a RecA-mediated self-cleavage reaction. UmuD', together with UmuC and activated RecA (RecA*), enables the DNA polymerase III holoenzyme to replicate across chemical and UV induced lesions. The efficiency of this reaction depends on several intricate protein-protein interactions.

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

Molecular function:

DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GeneOntology

serine-type peptidase activity Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). GeneOntology

Biological process:

proteolysis The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. GeneOntology

SOS response An error-prone process for repairing damaged microbial DNA. GeneOntology

regulation of transcription, DNA-templated Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GeneOntology

DNA repair The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. GeneOntology

Cellular component: not assigned

Structure Summary Structural annotations of the participating protein chains.

Entry contents: 2 distinct polypeptide molecules

Chains: A, B

Notes: No modifications of the original PDB file. Chain identifiers are identical with the PDB's identifiers.

Number of unique protein segments: 1

Chain A

Name: Protein UmuD

Source organism: Escherichia coli O157:H7

Length: 108 residues

Sequence:Sequence according to PDB SEQRESDYVEQRIDLNQLLIQHPSATYFVKASGDSMIDGGISDGDLLIVDSAITASHGDIVIAAVDGEFTVKKLQLRPTVQLIPMNSAYSPITISSEDTLDVFGVVIHVVKAMR

UniProtKB AC: P0AG12 (positions: 32-139) UniProt Coverage: 77.7%

UniRef90 AC: UniRef90_P0AG12 (positions: 32-139) UniRef90

Chain B

Name: Protein UmuD

Source organism: Escherichia coli O157:H7

Length: 108 residues

Sequence:Sequence according to PDB SEQRESDYVEQRIDLNQLLIQHPSATYFVKASGDSMIDGGISDGDLLIVDSAITASHGDIVIAAVDGEFTVKKLQLRPTVQLIPMNSAYSPITISSEDTLDVFGVVIHVVKAMR

UniProtKB AC: P0AG12 (positions: 32-139) UniProt Coverage: 77.7%

UniRef90 AC: UniRef90_P0AG12 (positions: 32-139) UniRef90

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

Chain A:

The 1-139 region described in DisProt entry DP00626 covers 100% of the sequence present in the structure.

Chain B:

The 1-139 region described in DisProt entry DP00626 covers 100% of the sequence present in the structure.

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).

There are 2 related structures in the Protein Data Bank:

• 1i4v
• 1umu

The molecule viewer shows the original PDB stucture.

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