Mistletoe lectin I in complex with galactose and lactose reveals distinct sugar-binding properties
The structures of mistletoe lectin I (ML‐I) from Viscum album complexed with lactose and galactose have been determined at 2.3 Å resolution and refined to R factors of 20.9% (Rfree = 23.6%) and 20.9 (Rfree = 24.6%), respectively. ML‐I is a heterodimer and belongs to the class of ribosome‐inactivatin...
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description | The structures of mistletoe lectin I (ML‐I) from Viscum album complexed with lactose and galactose have been determined at 2.3 Å resolution and refined to R factors of 20.9% (Rfree = 23.6%) and 20.9 (Rfree = 24.6%), respectively. ML‐I is a heterodimer and belongs to the class of ribosome‐inactivating proteins of type II, which consist of two chains. The A‐chain has rRNA N‐glycosidase activity and irreversibly inhibits eukaryotic ribosomes. The B‐chain is a lectin and preferentially binds to galactose‐terminated glycolipids and glycoproteins on cell membranes. Saccharide binding is performed by two binding sites in subdomains α1 and γ2 of the ML‐I B‐chain separated by ∼62 Å from each other. The favoured binding of galactose in subdomain α1 is achieved via hydrogen bonds connecting the 4‐hydroxyl and 3‐hydroxyl groups of the sugar moiety with the side chains of Asp23B, Gln36B and Lys41B and the main chain of 26B. The aromatic ring of Trp38B on top of the preferred binding pocket supports van der Waals packing of the apolar face of galactose and stabilizes the sugar–lectin complex. In the galactose‐binding site II of subdomain γ2, Tyr249B provides the hydrophobic stacking and the side chains of Asp235B, Gln238B and Asn256B are hydrogen‐bonding partners for galactose. In the case of the galactose‐binding site I, the 2‐hydroxyl group also stabilizes the sugar–protein complex, an interaction thus far rarely detected in galactose‐specific lectins. Finally, a potential third low‐affinity galactose‐binding site in subunit β1 was identified in the present ML‐I structures, in which a glycerol molecule from the cryoprotectant buffer has bound, mimicking the sugar compound. |
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ML‐I is a heterodimer and belongs to the class of ribosome‐inactivating proteins of type II, which consist of two chains. The A‐chain has rRNA N‐glycosidase activity and irreversibly inhibits eukaryotic ribosomes. The B‐chain is a lectin and preferentially binds to galactose‐terminated glycolipids and glycoproteins on cell membranes. Saccharide binding is performed by two binding sites in subdomains α1 and γ2 of the ML‐I B‐chain separated by ∼62 Å from each other. The favoured binding of galactose in subdomain α1 is achieved via hydrogen bonds connecting the 4‐hydroxyl and 3‐hydroxyl groups of the sugar moiety with the side chains of Asp23B, Gln36B and Lys41B and the main chain of 26B. The aromatic ring of Trp38B on top of the preferred binding pocket supports van der Waals packing of the apolar face of galactose and stabilizes the sugar–lectin complex. In the galactose‐binding site II of subdomain γ2, Tyr249B provides the hydrophobic stacking and the side chains of Asp235B, Gln238B and Asn256B are hydrogen‐bonding partners for galactose. In the case of the galactose‐binding site I, the 2‐hydroxyl group also stabilizes the sugar–protein complex, an interaction thus far rarely detected in galactose‐specific lectins. Finally, a potential third low‐affinity galactose‐binding site in subunit β1 was identified in the present ML‐I structures, in which a glycerol molecule from the cryoprotectant buffer has bound, mimicking the sugar compound.</description><identifier>ISSN: 1744-3091</identifier><identifier>EISSN: 1744-3091</identifier><identifier>DOI: 10.1107/S1744309104031501</identifier><identifier>PMID: 16508080</identifier><language>eng</language><publisher>5 Abbey Square, Chester, Cheshire CH1 2HU, England: Munksgaard International Publishers</publisher><subject>AFFINITY ; Amino Acid Sequence ; Binding Sites ; BONDING ; BUFFERS ; CHAINS ; CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY ; FASTENING ; Galactose - chemistry ; GLYCEROL ; HYDROGEN ; INTERACTIONS ; Lactose - chemistry ; Mistletoe ; mistletoe lectin I ; Models, Molecular ; Molecular Sequence Data ; MOLECULES ; Plant Preparations - chemistry ; Plant Proteins - chemistry ; POTENTIALS ; Protein Structure Communications ; Protein Structure, Secondary ; R FACTORS ; Ribosome Inactivating Proteins, Type 2 ; ribosome-inactivation proteins ; RINGS ; SACCHAROSE ; Sequence Alignment ; Sequence Homology, Amino Acid ; STOWING ; sugar-binding sites ; Toxins, Biological - chemistry</subject><ispartof>Acta crystallographica. Section F, Structural biology and crystallization communications, 2005-01, Vol.61 (1), p.17-25</ispartof><rights>International Union of Crystallography 2005 2005</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5136-c323f2bac54bbd0f3d56897976e0d309ed02065e0f874140fe3c0a6e27795cbe3</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952410/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952410/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,723,776,780,881,1411,27901,27902,45550,45551,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16508080$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/22356100$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Mikeska, Ruth</creatorcontrib><creatorcontrib>Wacker, Roland</creatorcontrib><creatorcontrib>Arni, Raghuvir</creatorcontrib><creatorcontrib>Singh, Tej P.</creatorcontrib><creatorcontrib>Mikhailov, Albert</creatorcontrib><creatorcontrib>Gabdoulkhakov, Azat</creatorcontrib><creatorcontrib>Voelter, Wolfgang</creatorcontrib><creatorcontrib>Betzel, Christian</creatorcontrib><title>Mistletoe lectin I in complex with galactose and lactose reveals distinct sugar-binding properties</title><title>Acta crystallographica. Section F, Structural biology and crystallization communications</title><addtitle>Acta Cryst. F</addtitle><description>The structures of mistletoe lectin I (ML‐I) from Viscum album complexed with lactose and galactose have been determined at 2.3 Å resolution and refined to R factors of 20.9% (Rfree = 23.6%) and 20.9 (Rfree = 24.6%), respectively. ML‐I is a heterodimer and belongs to the class of ribosome‐inactivating proteins of type II, which consist of two chains. The A‐chain has rRNA N‐glycosidase activity and irreversibly inhibits eukaryotic ribosomes. The B‐chain is a lectin and preferentially binds to galactose‐terminated glycolipids and glycoproteins on cell membranes. Saccharide binding is performed by two binding sites in subdomains α1 and γ2 of the ML‐I B‐chain separated by ∼62 Å from each other. The favoured binding of galactose in subdomain α1 is achieved via hydrogen bonds connecting the 4‐hydroxyl and 3‐hydroxyl groups of the sugar moiety with the side chains of Asp23B, Gln36B and Lys41B and the main chain of 26B. The aromatic ring of Trp38B on top of the preferred binding pocket supports van der Waals packing of the apolar face of galactose and stabilizes the sugar–lectin complex. In the galactose‐binding site II of subdomain γ2, Tyr249B provides the hydrophobic stacking and the side chains of Asp235B, Gln238B and Asn256B are hydrogen‐bonding partners for galactose. In the case of the galactose‐binding site I, the 2‐hydroxyl group also stabilizes the sugar–protein complex, an interaction thus far rarely detected in galactose‐specific lectins. Finally, a potential third low‐affinity galactose‐binding site in subunit β1 was identified in the present ML‐I structures, in which a glycerol molecule from the cryoprotectant buffer has bound, mimicking the sugar compound.</description><subject>AFFINITY</subject><subject>Amino Acid Sequence</subject><subject>Binding Sites</subject><subject>BONDING</subject><subject>BUFFERS</subject><subject>CHAINS</subject><subject>CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY</subject><subject>FASTENING</subject><subject>Galactose - chemistry</subject><subject>GLYCEROL</subject><subject>HYDROGEN</subject><subject>INTERACTIONS</subject><subject>Lactose - chemistry</subject><subject>Mistletoe</subject><subject>mistletoe lectin I</subject><subject>Models, Molecular</subject><subject>Molecular Sequence Data</subject><subject>MOLECULES</subject><subject>Plant Preparations - chemistry</subject><subject>Plant Proteins - chemistry</subject><subject>POTENTIALS</subject><subject>Protein Structure Communications</subject><subject>Protein Structure, Secondary</subject><subject>R FACTORS</subject><subject>Ribosome Inactivating Proteins, Type 2</subject><subject>ribosome-inactivation proteins</subject><subject>RINGS</subject><subject>SACCHAROSE</subject><subject>Sequence Alignment</subject><subject>Sequence Homology, Amino Acid</subject><subject>STOWING</subject><subject>sugar-binding sites</subject><subject>Toxins, Biological - chemistry</subject><issn>1744-3091</issn><issn>1744-3091</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFUV1rFDEUHUSxtfoDfJGA4NvYm2Qm2XkRytJuC21FVIpPIZO5sxudTaZJth__3iyzrRUfJJBcbs45NyenKN5S-EgpyMOvVFYVh4ZCBZzWQJ8V-9tWue09f1LvFa9i_AnAeSNmL4s9KmqY5bVftBc2pgGTRzKgSdaRM5I349fjgHfk1qYVWepBm-QjEu068lAHvEE9RNJlAetMInGz1KFsreusW5Ix-BFDshhfFy_6DMQ3u_Og-H5y_G1-Wp5_XpzNj85LU1MuSsMZ71mrTV21bQc972oxa2QjBUKXTWAHDESN0M9kRSvokRvQApmUTW1a5AfFp0l33LRr7Ay6FPSgxmDXOtwrr636-8bZlVr6G0WbmlUUssD7ScBnRyoam9CsjHcuf4xijNeCwhb1YTcm-OsNxqTWNhocBu3Qb6KSQFkDTZWBdAKa4GMM2D8-hYLa5qf-yS9z3j318IexCywDmglwawe8_7-iOvpxwo4vM1tkbjlxc2J498jV4ZcSkstaXV0u1BW9mC9OvzC14L8BMdG2XA</recordid><startdate>200501</startdate><enddate>200501</enddate><creator>Mikeska, Ruth</creator><creator>Wacker, Roland</creator><creator>Arni, Raghuvir</creator><creator>Singh, Tej P.</creator><creator>Mikhailov, Albert</creator><creator>Gabdoulkhakov, Azat</creator><creator>Voelter, Wolfgang</creator><creator>Betzel, Christian</creator><general>Munksgaard International Publishers</general><general>International Union of Crystallography</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>OTOTI</scope><scope>5PM</scope></search><sort><creationdate>200501</creationdate><title>Mistletoe lectin I in complex with galactose and lactose reveals distinct sugar-binding properties</title><author>Mikeska, Ruth ; Wacker, Roland ; Arni, Raghuvir ; Singh, Tej P. ; Mikhailov, Albert ; Gabdoulkhakov, Azat ; Voelter, Wolfgang ; Betzel, Christian</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5136-c323f2bac54bbd0f3d56897976e0d309ed02065e0f874140fe3c0a6e27795cbe3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>AFFINITY</topic><topic>Amino Acid Sequence</topic><topic>Binding Sites</topic><topic>BONDING</topic><topic>BUFFERS</topic><topic>CHAINS</topic><topic>CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY</topic><topic>FASTENING</topic><topic>Galactose - chemistry</topic><topic>GLYCEROL</topic><topic>HYDROGEN</topic><topic>INTERACTIONS</topic><topic>Lactose - chemistry</topic><topic>Mistletoe</topic><topic>mistletoe lectin I</topic><topic>Models, Molecular</topic><topic>Molecular Sequence Data</topic><topic>MOLECULES</topic><topic>Plant Preparations - chemistry</topic><topic>Plant Proteins - chemistry</topic><topic>POTENTIALS</topic><topic>Protein Structure Communications</topic><topic>Protein Structure, Secondary</topic><topic>R FACTORS</topic><topic>Ribosome Inactivating Proteins, Type 2</topic><topic>ribosome-inactivation proteins</topic><topic>RINGS</topic><topic>SACCHAROSE</topic><topic>Sequence Alignment</topic><topic>Sequence Homology, Amino Acid</topic><topic>STOWING</topic><topic>sugar-binding sites</topic><topic>Toxins, Biological - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mikeska, Ruth</creatorcontrib><creatorcontrib>Wacker, Roland</creatorcontrib><creatorcontrib>Arni, Raghuvir</creatorcontrib><creatorcontrib>Singh, Tej P.</creatorcontrib><creatorcontrib>Mikhailov, Albert</creatorcontrib><creatorcontrib>Gabdoulkhakov, Azat</creatorcontrib><creatorcontrib>Voelter, Wolfgang</creatorcontrib><creatorcontrib>Betzel, Christian</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Acta crystallographica. Section F, Structural biology and crystallization communications</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mikeska, Ruth</au><au>Wacker, Roland</au><au>Arni, Raghuvir</au><au>Singh, Tej P.</au><au>Mikhailov, Albert</au><au>Gabdoulkhakov, Azat</au><au>Voelter, Wolfgang</au><au>Betzel, Christian</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Mistletoe lectin I in complex with galactose and lactose reveals distinct sugar-binding properties</atitle><jtitle>Acta crystallographica. Section F, Structural biology and crystallization communications</jtitle><addtitle>Acta Cryst. F</addtitle><date>2005-01</date><risdate>2005</risdate><volume>61</volume><issue>1</issue><spage>17</spage><epage>25</epage><pages>17-25</pages><issn>1744-3091</issn><eissn>1744-3091</eissn><abstract>The structures of mistletoe lectin I (ML‐I) from Viscum album complexed with lactose and galactose have been determined at 2.3 Å resolution and refined to R factors of 20.9% (Rfree = 23.6%) and 20.9 (Rfree = 24.6%), respectively. ML‐I is a heterodimer and belongs to the class of ribosome‐inactivating proteins of type II, which consist of two chains. The A‐chain has rRNA N‐glycosidase activity and irreversibly inhibits eukaryotic ribosomes. The B‐chain is a lectin and preferentially binds to galactose‐terminated glycolipids and glycoproteins on cell membranes. Saccharide binding is performed by two binding sites in subdomains α1 and γ2 of the ML‐I B‐chain separated by ∼62 Å from each other. The favoured binding of galactose in subdomain α1 is achieved via hydrogen bonds connecting the 4‐hydroxyl and 3‐hydroxyl groups of the sugar moiety with the side chains of Asp23B, Gln36B and Lys41B and the main chain of 26B. The aromatic ring of Trp38B on top of the preferred binding pocket supports van der Waals packing of the apolar face of galactose and stabilizes the sugar–lectin complex. In the galactose‐binding site II of subdomain γ2, Tyr249B provides the hydrophobic stacking and the side chains of Asp235B, Gln238B and Asn256B are hydrogen‐bonding partners for galactose. In the case of the galactose‐binding site I, the 2‐hydroxyl group also stabilizes the sugar–protein complex, an interaction thus far rarely detected in galactose‐specific lectins. Finally, a potential third low‐affinity galactose‐binding site in subunit β1 was identified in the present ML‐I structures, in which a glycerol molecule from the cryoprotectant buffer has bound, mimicking the sugar compound.</abstract><cop>5 Abbey Square, Chester, Cheshire CH1 2HU, England</cop><pub>Munksgaard International Publishers</pub><pmid>16508080</pmid><doi>10.1107/S1744309104031501</doi><tpages>9</tpages><oa>free_for_read</oa></addata></record> |
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subjects | AFFINITY Amino Acid Sequence Binding Sites BONDING BUFFERS CHAINS CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY FASTENING Galactose - chemistry GLYCEROL HYDROGEN INTERACTIONS Lactose - chemistry Mistletoe mistletoe lectin I Models, Molecular Molecular Sequence Data MOLECULES Plant Preparations - chemistry Plant Proteins - chemistry POTENTIALS Protein Structure Communications Protein Structure, Secondary R FACTORS Ribosome Inactivating Proteins, Type 2 ribosome-inactivation proteins RINGS SACCHAROSE Sequence Alignment Sequence Homology, Amino Acid STOWING sugar-binding sites Toxins, Biological - chemistry |
title | Mistletoe lectin I in complex with galactose and lactose reveals distinct sugar-binding properties |
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