Database accession: MF7000620
Name: Lactococcus lactis ZitR, E41A mutant
PDB ID: 5yhz
Experimental method: X-ray (1.90 Å)
Assembly: Homodimer
Source organism: Lactococcus lactis subsp lactis
Primary publication of the structure:
Zhu R, Song Y, Liu H, Yang Y, Wang S, Yi C, Chen PR
Allosteric histidine switch for regulation of intracellular zinc(II) fluctuation.
(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 13661-13666
PMID: 29229866
Abstract:
Metalloregulators allosterically control transcriptional activity through metal binding-induced reorganization of ligand residues and/or hydrogen bonding networks, while the coordination atoms on the same ligand residues remain seldom changed. Here we show that the MarR-type zinc transcriptional regulator ZitR switches one of its histidine nitrogen atoms for zinc coordination during the allosteric control of DNA binding. The Zn(II)-coordination nitrogen on histidine 42 within ZitR's high-affinity zinc site (site 1) switches from Nε2 to Nδ1 upon Zn(II) binding to its low-affinity zinc site (site 2), which facilitates ZitR's conversion from the nonoptimal to the optimal DNA-binding conformation. This histidine switch-mediated cooperation between site 1 and site 2 enables ZitR to adjust its DNA-binding affinity in response to a broad range of zinc fluctuation, which may allow the fine tuning of transcriptional regulation.
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
zinc ion binding zinc ion binding
Biological process: not assigned
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: Zinc transport transcriptional regulator
Source organism: Lactococcus lactis subsp lactis
Length: 145 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSLANQIDQFLGTIMQFAENKHEILLGKCESDVKLTSTQEHILMLLAEQISTNAKIAEKLKISPAAVTKALKKLQEQELIKSSRATNDERVVLWSLTEKAVPVAKEHATHHEKTLSTYQELGNKFTDEEQEVISKFLSALTEEFQ
UniProtKB AC: Q9CDU5 (positions: 1-145)
Coverage: 100%
Name: Zinc transport transcriptional regulator
Source organism: Lactococcus lactis subsp lactis
Length: 145 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSLANQIDQFLGTIMQFAENKHEILLGKCESDVKLTSTQEHILMLLAEQISTNAKIAEKLKISPAAVTKALKKLQEQELIKSSRATNDERVVLWSLTEKAVPVAKEHATHHEKTLSTYQELGNKFTDEEQEVISKFLSALTEEFQ
UniProtKB AC: Q9CDU5 (positions: 1-145)
Coverage: 100%
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)
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