Database accession: MF7000626
Name: MarR family transcriptional regulator with benzoic acid (Variovorax paradoxus)
PDB ID: 7kfs
Experimental method: X-ray (1.50 Å)
Assembly: Homodimer
Source organism: Variovorax paradoxus
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 DNA binding
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, A-2
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: Variovorax paradoxus
Length: 158 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAEQPPETHRFVDDYLPALLAQASQLISSEFHEVARQHGFSVSEWRVMASLAGSEPISIGQLAQVTVTKQPTVTRLLDRMEARGQVERLPHESDRRITLVRITRKGLKAVEHLMELAREHERRVLEPFGLRRAEELKQTLRQMIDLHVHVPVEEPEED
UniProtKB AC: C5CSP2 (positions: 10-149)
Coverage: 88%
Name: Transcriptional regulator, MarR family
Source organism: Variovorax paradoxus
Length: 158 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAEQPPETHRFVDDYLPALLAQASQLISSEFHEVARQHGFSVSEWRVMASLAGSEPISIGQLAQVTVTKQPTVTRLLDRMEARGQVERLPHESDRRITLVRITRKGLKAVEHLMELAREHERRVLEPFGLRRAEELKQTLRQMIDLHVHVPVEEPEED
UniProtKB AC: C5CSP2 (positions: 10-149)
Coverage: 88%
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 A-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)
Download this entry's JSON file (.json)
