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      Ca 2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice

      research-article
      * , , * , , * , * , 1
      Bioscience Reports
      Portland Press Ltd.
      bacterial Ig-like fold, Ca2+-binding, crystal structure, extender domain, ice-binding adhesin, solution structure, aa, amino acid, AFP, antifreeze protein, AUC, analytical ultracentrifugation, BIg, bacterial immunoglobulin, MpAFP, Marinomonas primoryensis antifreeze protein, ORF, open reading frame, RDF, radial distribution function, RII, Region II, RII tetra-tandemer, four tandem RII, RIV, repetitive Region IV, RTX, repeats-in-toxin, SAXS, small-angle X-ray scattering, TISS, type I secretion system, WLC, worm-like chain, XRD, X-ray diffraction

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          Abstract

          The large size of a 1.5-MDa ice-binding adhesin [ MpAFP ( Marinomonas primoryensis antifreeze protein)] from an Antarctic Gram-negative bacterium, M. primoryensis, is mainly due to its highly repetitive RII (Region II). MpAFP_RII contains roughly 120 tandem copies of an identical 104-residue repeat. We have previously determined that a single RII repeat folds as a Ca 2+-dependent immunoglobulin-like domain. Here, we solved the crystal structure of RII tetra-tandemer (four tandem RII repeats) to a resolution of 1.8 Å. The RII tetra-tandemer reveals an extended (~190-Å × ~25-Å), rod-like structure with four RII-repeats aligned in series with each other. The inter-repeat regions of the RII tetra-tandemer are strengthened by Ca 2+ bound to acidic residues. SAXS (small-angle X-ray scattering) profiles indicate the RII tetra-tandemer is significantly rigidified upon Ca 2+ binding, and that the protein's solution structure is in excellent agreement with its crystal structure. We hypothesize that >600 Ca 2+ help rigidify the chain of ~120 104-residue repeats to form a ~0.6 μm rod-like structure in order to project the ice-binding domain of MpAFP away from the bacterial cell surface. The proposed extender role of RII can help the strictly aerobic, motile bacterium bind ice in the upper reaches of the Antarctic lake where oxygen and nutrients are most abundant. Ca 2+-induced rigidity of tandem Ig-like repeats in large adhesins might be a general mechanism used by bacteria to bind to their substrates and help colonize specific niches.

          Abstract

          An Antarctic bacterium, Marinomonas primoryensis, uses a 1.5-MDa adhesin to bind ice. Crystal and solution structures of four of its 120 tandem Ig-like repeats show how Ca 2+ rigidifies and projects the adhesin from the bacteria to the ice.

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          Most cited references28

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          REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use.

          One of the most important aspects of macromolecular structure refinement is the use of prior chemical knowledge. Bond lengths, bond angles and other chemical properties are used in restrained refinement as subsidiary conditions. This contribution describes the organization and some aspects of the use of the flexible and human/machine-readable dictionary of prior chemical knowledge used by the maximum-likelihood macromolecular-refinement program REFMAC5. The dictionary stores information about monomers which represent the constitutive building blocks of biological macromolecules (amino acids, nucleic acids and saccharides) and about numerous organic/inorganic compounds commonly found in macromolecular crystallography. It also describes the modifications the building blocks undergo as a result of chemical reactions and the links required for polymer formation. More than 2000 monomer entries, 100 modification entries and 200 link entries are currently available. Algorithms and tools for updating and adding new entries to the dictionary have also been developed and are presented here. In many cases, the REFMAC5 dictionary allows entirely automatic generation of restraints within REFMAC5 refinement runs.
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            Optimal description of a protein structure in terms of multiple groups undergoing TLS motion.

            A single protein crystal structure contains information about dynamic properties of the protein as well as providing a static view of one three-dimensional conformation. This additional information is to be found in the distribution of observed electron density about the mean position of each atom. It is general practice to account for this by refining a separate atomic displacement parameter (ADP) for each atomic center. However, these same displacements are often described well by simpler models based on TLS (translation/libration/screw) rigid-body motion of large groups of atoms, for example interdomain hinge motion. A procedure, TLSMD, has been developed that analyzes the distribution of ADPs in a previously refined protein crystal structure in order to generate optimal multi-group TLS descriptions of the constituent protein chains. TLSMD is applicable to crystal structures at any resolution. The models generated by TLSMD analysis can significantly improve the standard crystallographic residuals R and R(free) and can reveal intrinsic dynamic properties of the protein.
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              CRYSOL– a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates

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                Author and article information

                Journal
                Biosci Rep
                Biosci. Rep
                bsr
                BSR
                Bioscience Reports
                Portland Press Ltd.
                0144-8463
                1573-4935
                3 June 2014
                4 July 2014
                2014
                : 34
                : 4
                : e00121
                Affiliations
                *Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
                †Laboratory of Macromolecular and Organic Chemistry and Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
                Author notes

                Structural data are available in the Protein Data Bank under the accession number of 4P99.

                1To correspondence should be addressed (email guo.shuaiqi@ 123456queensu.ca ).
                Article
                e00121
                10.1042/BSR20140083
                4083281
                24892750
                9ba98586-178c-4cdc-8f5f-9106f5b9b113
                © 2014 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Licence (CC-BY) (http://creativecommons.org/licenses/by/3.0/) which permits unrestricted use, distribution and reproduction in any medium, provided the original work is properly cited.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Licence (CC-BY) ( http://creativecommons.org/licenses/by/3.0/) which permits unrestricted use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 29 May 2014
                : 3 June 2014
                Page count
                Figures: 7, Tables: 3, References: 43, Pages: 12
                Categories
                Original Paper
                S2

                Life sciences
                bacterial ig-like fold,ca2+-binding,crystal structure,extender domain,ice-binding adhesin,solution structure,aa, amino acid,afp, antifreeze protein,auc, analytical ultracentrifugation,big, bacterial immunoglobulin,mpafp, marinomonas primoryensis antifreeze protein,orf, open reading frame,rdf, radial distribution function,rii, region ii,rii tetra-tandemer, four tandem rii,riv, repetitive region iv,rtx, repeats-in-toxin,saxs, small-angle x-ray scattering,tiss, type i secretion system,wlc, worm-like chain,xrd, x-ray diffraction

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