Investigation of non-corrin cobalt(II)-containing sites in protein structures of the Protein Data Bank

Abriata, Luciano A.

doi:10.1107/s0108768113002954

Cited by 2 publications

(7 citation statements)

References 33 publications

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“…Using the “Low resolution adjustment” option will not change the calculated parameters for each site, but will change the thresholds used to distinguish the outlier-borderline-acceptable ranges as indicated by red-amber-green background colors. This option will only affect structures with a resolution worse than 2 Å 10,16 . ▲ CRITICAL STEP The authors suggest that less experienced users not use this option. As metal coordination chemistry itself obviously does not depend on the resolution of structural data, the consideration of resolution in the evaluation of metal binding site quality is questionable in itself.…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…Incorrect metal assignments in structures of biological macromolecules may cause the misinterpretation of molecular mechanisms and distort bioinformatics studies of living systems. Despite advances in software applications 7,8 incorporating new refinement and validation protocols 9 , the modeling of metal binding sites is not improving 1,10 . The overall trend shows that the percentage of erroneous metal binding sites (as defined below) has stayed similar or even increased over the past 30 years (Fig.…”

Section: Introductionmentioning

confidence: 99%

“…As a consequence, artifacts in metal binding site modeling are frequent. For example, the coordination bond distances were shown to vary significantly in a resolution-dependent manner for zinc 16 and cobalt 10 . In a more elaborate model, coordination bond distances for copper 17 and cobalt 10 also appeared to be related to the specific coordination sphere composition in addition to the ligand element.…”

Section: Introductionmentioning

confidence: 99%

“…For example, the coordination bond distances were shown to vary significantly in a resolution-dependent manner for zinc 16 and cobalt 10 . In a more elaborate model, coordination bond distances for copper 17 and cobalt 10 also appeared to be related to the specific coordination sphere composition in addition to the ligand element. This highlights the fact that correct metal placement is not trivial and is highly subjective to the experience of the structural biologist building the model 6 .…”

Section: Introductionmentioning

confidence: 99%

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Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server

et al. 2013

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Metals play vital roles in both the mechanism and architecture of biological macromolecules. Yet structures of metal-containing macromolecules where metals are misidentified and/or suboptimally modeled are abundant in the Protein Data Bank (PDB). This shows the need for a diagnostic tool to identify and correct such modeling problems with metal binding environments. The "CheckMyMetal" (CMM) web server (http://csgid.org/csgid/metal_sites/) is a sophisticated, user-friendly web-based method to evaluate metal binding sites in macromolecular structures in respect to 7350 metal binding sites observed in a benchmark dataset of 2304 high resolution crystal structures. The protocol outlines how the CMM server can be used to detect geometric and other irregularities in the structures of metal binding sites and alert researchers to potential errors in metal assignment. The protocol also gives practical guidelines for correcting problematic sites by modifying the metal binding environment and/or redefining metal identity in the PDB file. Several examples where this has led to meaningful results are described in the anticipated results section. CMM was designed for a broad audience—biomedical researchers studying metal-containing proteins and nucleic acids—but is equally well suited for structural biologists to validate new structures during modeling or refinement. The CMM server takes the coordinates of a metal-containing macromolecule structure in the PDB format as input and responds within a few seconds for a typical protein structure modeled with a few hundred amino acids.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server

et al. 2013

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Metallochaperone function of the self‐subunit swapping chaperone involved in the maturation of subunit‐fused cobalt‐type nitrile hydratase

Xia

Pepłowski

Cheng

et al. 2019

Biotech & Bioengineering

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The transition metal (iron or cobalt) is a mandatory part that constitutes the catalytic center of nitrile hydratase (NHase). The incorporation of the cobalt ion into cobalt‐containing NHase (Co‐NHase) was reported to depend on self‐subunit swapping and the activator of the Co‐NHase acts as a self‐subunit swapping chaperone for subunit exchange. Here we discovered that the activator acting as a metallochaperone transferred the cobalt ion into subunit‐fused Co‐NHase. We successfully isolated two activators, P14K and NhlE, which were the activators of NHases from Pseudomonas putida NRRL‐18668 and the activator of low‐molecular‐mass NHase from Rhodococcus rhodochrous J1, respectively. Cobalt content determination demonstrated that NhlE and P14K were two cobalt‐containing proteins. Substitution of the amino acids involved in the C‐terminus of the activators affected the activity of the two NHases, indicating that the potential cobalt‐binding sites might be located at the flexible C‐terminal region. The cobalt‐free NHases could be activated by either of the two activators, and both the two activators activated their cognate NHase more efficiently than did the noncognate ones. This study provided insights into the maturation of subunit‐fused NHases and confirmed the metallochaperone function of the self‐subunit swapping chaperone.

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Investigation of non-corrin cobalt(II)-containing sites in protein structures of the Protein Data Bank

Cited by 2 publications

References 33 publications

Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server

Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server

Metallochaperone function of the self‐subunit swapping chaperone involved in the maturation of subunit‐fused cobalt‐type nitrile hydratase

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