Database accession: MF7000246
Name: Transcriptional regulator SlyA (Enterococcus faecalis)
PDB ID: 1lj9
Experimental method: X-ray (1.60 Å)
Assembly: Homodimer
Source organism: Enterococcus faecalis
Primary publication of the structure:
Wu RY, Zhang RG, Zagnitko O, Dementieva I, Maltzev N, Watson JD, Laskowski R, Gornicki P, Joachimiak A
Crystal structure of Enterococcus faecalis SlyA-like transcriptional factor.
(2003) J. Biol. Chem. 278: 20240-4
PMID: 12649270
Abstract:
The crystal structure of a SlyA transcriptional regulator at 1.6 A resolution is presented, and structural relationships between members of the MarR/SlyA family are discussed. The SlyA family, which includes SlyA, Rap, Hor, and RovA proteins, is widely distributed in bacterial and archaeal genomes. Current evidence suggests that SlyA-like factors act as repressors, activators, and modulators of gene transcription. These proteins have been shown to up-regulate the expression of molecular chaperones, acid-resistance proteins, and cytolysin, and down-regulate several biosynthetic enzymes. The structure of SlyA from Enterococcus faecalis, determined as a part of an ongoing structural genomics initiative (www.mcsg.anl.gov), revealed the same winged helix DNA-binding motif that was recently found in the MarR repressor from Escherichia coli and the MexR repressor from Pseudomonas aeruginosa, a sequence homologue of MarR. Phylogenetic analysis of the MarR/SlyA family suggests that Sly is placed between the SlyA and MarR subfamilies and shows significant sequence similarity to members of both subfamilies.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
DNA-binding transcription factor activity DNA-binding transcription factor activity
Biological process: not assigned
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Transcriptional regulator, MarR family
Source organism: Enterococcus faecalis
Length: 150 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMTDILREIGMIARALDSISNIEFKELSLTRGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPIIVRENQHSNQVALQGLSEVEISQLADYLVRMRKNVSEDWEFVKKGNTRNY
UniProtKB AC: Q82ZP8 (positions: 2-145)
Coverage: 96%
Name: Transcriptional regulator, MarR family
Source organism: Enterococcus faecalis
Length: 150 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMTDILREIGMIARALDSISNIEFKELSLTRGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPIIVRENQHSNQVALQGLSEVEISQLADYLVRMRKNVSEDWEFVKKGNTRNY
UniProtKB AC: Q82ZP8 (positions: 2-143)
Coverage: 94%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Winged helix DNA-binding domain (MarR type I) transcriptional regulator
Evidence level: Direct evidence
Evidence coverage: Only some parts of the structure participates in mutual synergistic folding.
Complex Evidence:
The MarR-type family transcriptional regulator, NadR is dimeric in solution (SE-HPLC/MALLS) as other MarR faimily proteins (PMID:18272181). Compared to ligand-stabilized holo-NadR, apo-NadR displayed an intrinsic flexibility focused in the DNA-binding region (PMID:27105075). The structural features of several family members have been described, they all have two subdomains: there is a helix-turn-helix (HTH) DNA-binding domain plus dimerization helices that form an interlocked dimerization domain. Dimerization is mediated by helices α1, α5, and α6 from each monomer resulting in an interlocked, tight dimer burying a large, hydrophobic solvent-accessible surface area. The structure of the dimerization region reveals domain swapping, where α1 of one subunit is inserted between α5′ and α6′ of the other subunit and forms a coiled coil with helix α6′ (PMID:19586910). The DNA-binding elements contain helices α3-α4 and strands β1-β2 from each monomer (PMID:29794028, PMID:35367827).
Chain A:
N/A
Chain B:
N/A
Surface and contacts features:
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). Download the CIF file (.cif)
Download this entry's XML file (.xml)
Download this entry's JSON file (.json)
