6MI5 | pdb_00006mi5

NMR solution structure of lanmodulin (LanM) complexed with yttrium(III) ions


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 12 
  • Conformers Submitted: 12 
  • Selection Criteria: structures with acceptable covalent geometry 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural Basis for Rare Earth Element Recognition by Methylobacterium extorquens Lanmodulin.

Cook, E.C.Featherston, E.R.Showalter, S.A.Cotruvo Jr., J.A.

(2019) Biochemistry 58: 120-125

  • DOI: https://doi.org/10.1021/acs.biochem.8b01019
  • Primary Citation Related Structures: 
    6MI5

  • PubMed Abstract: 

    Lanmodulin (LanM) is a high-affinity lanthanide (Ln)-binding protein recently identified in Methylobacterium extorquens, a bacterium that requires Lns for the function of at least two enzymes. LanM possesses four EF-hands, metal coordination motifs generally associated with Ca II binding, but it undergoes a metal-dependent conformational change with a 100 million-fold selectivity for Ln III s and Y III over Ca II . Here we present the nuclear magnetic resonance solution structure of LanM complexed with Y III . This structure reveals that LanM features an unusual fusion of adjacent EF-hands, resulting in a compact fold to the best of our knowledge unique among EF-hand-containing proteins. It also supports the importance of an additional carboxylate ligand in contributing to the protein's picomolar affinity for Ln III s, and it suggests a role of unusual N i+1 -H···N i hydrogen bonds, in which LanM's unique EF-hand proline residues are engaged, in selective Ln III recognition. This work sets the stage for a detailed mechanistic understanding of LanM's Ln selectivity, which may inspire new strategies for binding, detecting, and sequestering these technologically important metals.


  • Organizational Affiliation
    • Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States.

Macromolecule Content 

  • Total Structure Weight: 12.8 kDa 
  • Atom Count: 885 
  • Modeled Residue Count: 117 
  • Deposited Residue Count: 117 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LanmodulinA [auth X]117Methylorubrum extorquens AM1Mutation(s): 0 
Gene Names: MexAM1_META1p1786
UniProt
Find proteins for C5B164 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1))
Explore C5B164 
Go to UniProtKB:  C5B164
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC5B164
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 12 
  • Conformers Submitted: 12 
  • Selection Criteria: structures with acceptable covalent geometry 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2019-02-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Derived calculations