Database accession: MF7000256
Name: MarR (Bradyrhizobium japonicum)
PDB ID: 7kym
Experimental method: X-ray (1.50 Å)
Assembly: Homodimer
Source organism: Bradyrhizobium japonicum
Primary publication of the structure:
Conway JM, Walton WG, Salas-González I, Law TF, Lindberg CA, Crook LE, Kosina SM, Fitzpatrick CR, Lietzan AD, Northen TR, Jones CD, Finkel OM, Redinbo MR, Dangl JL
Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome.
(2022) Nat Microbiol 7: 1817-1833
PMID: 36266335
Abstract:
Chemical signalling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via an auxin degradation locus was essential for maintaining stereotypic root development in an ecologically relevant bacterial synthetic community. Here, we dissect the Variovorax auxin degradation locus to define the genes iadDE as necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon's MarR-family repressor with IAA and other auxins. Auxin degradation operons were identified across the bacterial tree of life and we define two distinct types on the basis of gene content and metabolic products: iac-like and iad-like. The structures of MarRs from representatives of each auxin degradation operon type establish that each has distinct IAA-binding pockets. Comparison of representative IAA-degrading strains from diverse bacterial genera colonizing Arabidopsis plants show that while all degrade IAA, only strains containing iad-like auxin-degrading operons interfere with auxin signalling in a complex synthetic community context. This suggests that iad-like operon-containing bacterial strains, including Variovorax species, play a key ecological role in modulating auxins in the plant microbiome.
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:
response to stress response to stress
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B-2
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: MarR family transcriptional regulator
Source organism: Bradyrhizobium japonicum
Length: 160 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMARESKSRWKSGPPRTRDQLQTYIPYLFNRLANRWNLDQNRDLSDHGINNVVFRTLSVLFIYKTLTVNEVAVLAVTEQSTASRMVESMVSSGLVKREIAEEDQRRRVVGLTPDGEALLRKIWPIMASNYDKLIEGIEPDDIEVCARVLARMVENIRQNQI
UniProtKB AC: A0A0A3XYM8 (positions: 9-160)
Coverage: 95%
Name: MarR family transcriptional regulator
Source organism: Bradyrhizobium japonicum
Length: 160 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMARESKSRWKSGPPRTRDQLQTYIPYLFNRLANRWNLDQNRDLSDHGINNVVFRTLSVLFIYKTLTVNEVAVLAVTEQSTASRMVESMVSSGLVKREIAEEDQRRRVVGLTPDGEALLRKIWPIMASNYDKLIEGIEPDDIEVCARVLARMVENIRQNQI
UniProtKB AC: A0A0A3XYM8 (positions: 12-160)
Coverage: 93%
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 II) transcriptional regulator
Evidence level: Indirect evidence
Evidence coverage: Only some parts of the structure participates in mutual synergistic folding.
Complex Evidence:
Thermal unfolding measured with circular dichroism of the MarR family protein, HucR, suggested two-state model of unfolding (PMID:15448166). Also, a decrease in pH induced a molten globule-like state, where the protein remained in dimeric form (PMID:27282811). Helices 1, 2, 6 and 7 form the dimerization subdomain, they form an apparently stable dimer interface that preconfigures the DNA recognition HTH subdomain for DNA binding (PMID:16750221).
Chain A:
N/A
Chain B-2:
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)
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