<i>CheckMyMetal</i>: a macromolecular metal-binding validation tool

Zheng, Heping; Cooper, David R.; Porebski, P.J.; Shabalin, I.G.; Handing, K.B.; Minor, Władek

doi:10.1107/s2059798317001061

Cited by 300 publications

(276 citation statements)

References 58 publications

Supporting

Mentioning

257

Contrasting

Unclassified

Order By: Relevance

“…Placement of sodium, also present in the crystallization conditions, resulted in strong positive difference electron density after subsequent rounds of refinement, confirming the likelihood of a more electron dense potassium ion at this location. Ligation distances and geometry are also similar to potassium ions in other protein structures [57]. The potassium ion binds on the surface of the protein at the interface between the N-terminal and C-terminal domains, where Asn20 Od1 coordinates (2.7 A) together with carbonyl oxygens from Thr597 (2.8 A) and Tyr599 (2.7 A) ( Fig.…”

Section: Maldi-tof Ms Analysis Of N-glycans Released From Rnase B Witsupporting

confidence: 59%

Enterococcus faecalis α1–2‐mannosidase (EfMan‐I): an efficient catalyst for glycoprotein N‐glycan modification

et al. 2019

FEBS Letters

View full text Add to dashboard Cite

While multiple α 1–2‐mannosidases are necessary for glycoprotein N‐glycan maturation in vertebrates, a single bacterial α1–2‐mannosidase can be sufficient to cleave all α1–2‐linked mannose residues in host glycoprotein N‐glycans. We report here the characterization and crystal structure of a new α1–2‐mannosidase (EfMan‐I) from Enterococcus faecalis, a Gram‐positive opportunistic human pathogen. EfMan‐I catalyzes the cleavage of α1–2‐mannose from not only oligomannoses but also high‐mannose‐type N‐glycans on glycoproteins. Its 2.15 Å resolution crystal structure reveals a two‐domain enzyme fold similar to other CAZy GH92 mannosidases. An unexpected potassium ion was observed bridging two domains near the active site. These findings support EfMan‐I as an effective catalyst for in vitro N‐glycan modification of glycoproteins with high‐mannose‐type N‐glycans.

show abstract

Section: Maldi-tof Ms Analysis Of N-glycans Released From Rnase B Witsupporting

confidence: 59%

Enterococcus faecalis α1–2‐mannosidase (EfMan‐I): an efficient catalyst for glycoprotein N‐glycan modification

et al. 2019

FEBS Letters

View full text Add to dashboard Cite

show abstract

“…A Na + ion was placed in EF3 of N98S Ca 2+ –CaM (chain A) because the electron density did not support a water molecule or other ions such as Ca 2+ , Mg 2+ or Ni 2+ (Zheng et al . 2017). Molecular graphics were prepared using PyMOL (http://www.pymol.org) (The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC).…”

Section: Methodsmentioning

confidence: 99%

Arrhythmia mutations in calmodulin can disrupt cooperativity of Ca²⁺ binding and cause misfolding

Wang

Brohus

Holt

et al. 2020

The Journal of Physiology

View full text Add to dashboard Cite

Key points Mutations in the calmodulin protein (CaM) are associated with arrhythmia syndromes. This study focuses on understanding the structural characteristics of CaM disease mutants and their interactions with the voltage‐gated calcium channel CaV1.2. Arrhythmia mutations in CaM can lead to loss of Ca2+ binding, uncoupling of Ca2+ binding cooperativity, misfolding of the EF‐hands and altered affinity for the calcium channel. These results help us to understand how different CaM mutants have distinct effects on structure and interactions with protein targets to cause disease. Abstract Calmodulinopathies are life‐threatening arrhythmia syndromes that arise from mutations in calmodulin (CaM), a calcium sensing protein whose sequence is completely conserved across all vertebrates. These mutations have been shown to interfere with the function of cardiac ion channels, including the voltage‐gated Ca2+ channel CaV1.2 and the ryanodine receptor (RyR2), in a mutation‐specific manner. The ability of different CaM disease mutations to discriminate between these channels has been enigmatic. We present crystal structures of several C‐terminal lobe mutants and an N‐terminal lobe mutant in complex with the CaV1.2 IQ domain, in conjunction with binding assays and complementary structural biology techniques. One mutation (D130G) causes a pathological conformation, with complete separation of EF‐hands within the C‐lobe and loss of Ca2+ binding in EF‐hand 4. Another variant (Q136P) has severely reduced affinity for the IQ domain, and shows changes in the CD spectra under Ca2+‐saturating conditions when unbound to the IQ domain. Ca2+ binding to a pair of EF‐hands normally proceeds with very high cooperativity, but we found that N98S CaM can adopt different conformations with either one or two Ca2+ ions bound to the C‐lobe, possibly disrupting the cooperativity. An N‐lobe variant (N54I), which causes severe stress‐induced arrhythmia, does not show any major changes in complex with the IQ domain, providing a structural basis for why this mutant does not affect function of CaV1.2. These findings show that different CaM mutants have distinct effects on both the CaM structure and interactions with protein targets, and act via distinct pathological mechanisms to cause disease.

show abstract

“…Manual model building was carried out in COOT (Emsley et al, 2010) and refined using refmac5 (Winn et al, 2003). Metal binding sites were validated using the CheckMyMetal server (Zheng et al, 2017). Polder (OMIT) maps were generated using the Polder Map module of Phenix (Adams et al, 2010;Liebschner et al, 2017).…”

Section: Differential Scanning Fluorimetrymentioning

confidence: 99%

An oligomeric state‐dependent switch in the ER enzyme FICD regulates AMP ylation and de AMP ylation of BiP

et al. 2019

View full text Add to dashboard Cite

AMPylation is an inactivating modification that alters the activity of the major endoplasmic reticulum (ER) chaperone BiP to match the burden of unfolded proteins. A single ER‐localised Fic protein, FICD (HYPE), catalyses both AMPylation and deAMPylation of BiP. However, the basis for the switch in FICD's activity is unknown. We report on the transition of FICD from a dimeric enzyme, that deAMPylates BiP, to a monomer with potent AMPylation activity. Mutations in the dimer interface, or of residues along an inhibitory pathway linking the dimer interface to the enzyme's active site, favour BiP AMPylation in vitro and in cells. Mechanistically, monomerisation relieves a repressive effect allosterically propagated from the dimer interface to the inhibitory Glu234, thereby permitting AMPylation‐competent binding of MgATP. Moreover, a reciprocal signal, propagated from the nucleotide‐binding site, provides a mechanism for coupling the oligomeric state and enzymatic activity of FICD to the energy status of the ER.

show abstract

CheckMyMetal: a macromolecular metal-binding validation tool

Cited by 300 publications

References 58 publications

Enterococcus faecalis α1–2‐mannosidase (EfMan‐I): an efficient catalyst for glycoprotein N‐glycan modification

Enterococcus faecalis α1–2‐mannosidase (EfMan‐I): an efficient catalyst for glycoprotein N‐glycan modification

Arrhythmia mutations in calmodulin can disrupt cooperativity of Ca²⁺ binding and cause misfolding

An oligomeric state‐dependent switch in the ER enzyme FICD regulates AMP ylation and de AMP ylation of BiP

Contact Info

Product

Resources

About

CheckMyMetal: a macromolecular metal-binding validation tool

Cited by 300 publications

References 58 publications

Enterococcus faecalis α1–2‐mannosidase (EfMan‐I): an efficient catalyst for glycoprotein N‐glycan modification

Enterococcus faecalis α1–2‐mannosidase (EfMan‐I): an efficient catalyst for glycoprotein N‐glycan modification

Arrhythmia mutations in calmodulin can disrupt cooperativity of Ca2+ binding and cause misfolding

An oligomeric state‐dependent switch in the ER enzyme FICD regulates AMP ylation and de AMP ylation of BiP

Contact Info

Product

Resources

About

Arrhythmia mutations in calmodulin can disrupt cooperativity of Ca²⁺ binding and cause misfolding