Analysis of surface binding sites (SBSs) in carbohydrate active enzymes with focus on glycoside hydrolase families 13 and 77

— a mini-review

Darrell Cockburn, Casper Wilkens, Christian Ruzanski, Susan Andersen, Jonas Willum Nielsen, Alison M. Smith, Robert A. Field, Martin Willemoes, Maher Abou Hachem, Birte Svensson

    Research output: Contribution to journalJournal articleResearchpeer-review

    Abstract

    Surface binding sites (SBSs) interact with carbohydrates outside of the enzyme active site. They are frequently situated on catalytic domains and are distinct from carbohydrate binding modules (CBMs). SBSs are found in a variety of enzymes and often seen in crystal structures. Notably about half of the > 45 enzymes (in 17 GH and two GT families) with an identified SBS are from GH13 and a few from GH77, both belonging to clan GH-H of carbohydrate active enzymes. The many enzymes of GH13 with SBSs provide an opportunity to analyse their distribution within this very large and diverse family. SBS containing enzymes in GH13 are spread among 15 subfamilies (two were not assigned a subfamily). Comparison of these SBSs reveals a complex evolutionary history with evidence of conservation of key residues and/or structural location between some SBSs, while others are found at entirely distinct structural locations, suggesting convergent evolution. An array of investigations of the two SBSs in barley α-amylase demonstrated they play different functional roles in binding and degradation of polysaccharides. MalQ from Escherichia coli is an α-1,4-glucanotransferase of GH77, a family that is known to have at least one member that contains an SBS. Whereas MalQ is a single domain enzyme lacking CBMs, its plant orthologue DPE2 contains two N-terminal CBM20s. Surface plasmon resonance binding studies showed that MalQ and DPE2 have a similar affinity for β-cyclodextrin and that MalQ binds malto-oligosaccharides of >DP4 at a second site in competition with β-cyclodextrin yielding a stoichiometry >1. This suggests that MalQ may have an SBS, though its structural location remains unknown.
    Original languageEnglish
    JournalBiologia
    Volume69
    Issue number6
    Pages (from-to)705-712
    Number of pages8
    ISSN0006-3088
    DOIs
    Publication statusPublished - 2014

    Keywords

    • HASH(0x53dca48)
    • Secondary binding sites
    • Carbohydrate binding modules
    • GH13 subfamilies
    • Crystal structures
    • Surface plasmon resonance
    • Affinity gel electrophoresis
    • Amylopectin hydrolysis kinetics

    Cite this

    Cockburn, Darrell ; Wilkens, Casper ; Ruzanski, Christian ; Andersen, Susan ; Willum Nielsen, Jonas ; Smith, Alison M. ; Field, Robert A. ; Willemoes, Martin ; Abou Hachem, Maher ; Svensson, Birte. / Analysis of surface binding sites (SBSs) in carbohydrate active enzymes with focus on glycoside hydrolase families 13 and 77 : — a mini-review. In: Biologia. 2014 ; Vol. 69, No. 6. pp. 705-712.
    @article{465dbfa13a22498da11d9a700c25497f,
    title = "Analysis of surface binding sites (SBSs) in carbohydrate active enzymes with focus on glycoside hydrolase families 13 and 77: — a mini-review",
    abstract = "Surface binding sites (SBSs) interact with carbohydrates outside of the enzyme active site. They are frequently situated on catalytic domains and are distinct from carbohydrate binding modules (CBMs). SBSs are found in a variety of enzymes and often seen in crystal structures. Notably about half of the > 45 enzymes (in 17 GH and two GT families) with an identified SBS are from GH13 and a few from GH77, both belonging to clan GH-H of carbohydrate active enzymes. The many enzymes of GH13 with SBSs provide an opportunity to analyse their distribution within this very large and diverse family. SBS containing enzymes in GH13 are spread among 15 subfamilies (two were not assigned a subfamily). Comparison of these SBSs reveals a complex evolutionary history with evidence of conservation of key residues and/or structural location between some SBSs, while others are found at entirely distinct structural locations, suggesting convergent evolution. An array of investigations of the two SBSs in barley α-amylase demonstrated they play different functional roles in binding and degradation of polysaccharides. MalQ from Escherichia coli is an α-1,4-glucanotransferase of GH77, a family that is known to have at least one member that contains an SBS. Whereas MalQ is a single domain enzyme lacking CBMs, its plant orthologue DPE2 contains two N-terminal CBM20s. Surface plasmon resonance binding studies showed that MalQ and DPE2 have a similar affinity for β-cyclodextrin and that MalQ binds malto-oligosaccharides of >DP4 at a second site in competition with β-cyclodextrin yielding a stoichiometry >1. This suggests that MalQ may have an SBS, though its structural location remains unknown.",
    keywords = "HASH(0x53dca48), Secondary binding sites, Carbohydrate binding modules, GH13 subfamilies, Crystal structures, Surface plasmon resonance, Affinity gel electrophoresis, Amylopectin hydrolysis kinetics",
    author = "Darrell Cockburn and Casper Wilkens and Christian Ruzanski and Susan Andersen and {Willum Nielsen}, Jonas and Smith, {Alison M.} and Field, {Robert A.} and Martin Willemoes and {Abou Hachem}, Maher and Birte Svensson",
    year = "2014",
    doi = "10.2478/s11756-014-0373-9",
    language = "English",
    volume = "69",
    pages = "705--712",
    journal = "Biologia",
    issn = "0006-3088",
    publisher = "Walterde Gruyter GmbH",
    number = "6",

    }

    Analysis of surface binding sites (SBSs) in carbohydrate active enzymes with focus on glycoside hydrolase families 13 and 77 : — a mini-review. / Cockburn, Darrell; Wilkens, Casper; Ruzanski, Christian; Andersen, Susan; Willum Nielsen, Jonas; Smith, Alison M.; Field, Robert A.; Willemoes, Martin; Abou Hachem, Maher ; Svensson, Birte.

    In: Biologia, Vol. 69, No. 6, 2014, p. 705-712.

    Research output: Contribution to journalJournal articleResearchpeer-review

    TY - JOUR

    T1 - Analysis of surface binding sites (SBSs) in carbohydrate active enzymes with focus on glycoside hydrolase families 13 and 77

    T2 - — a mini-review

    AU - Cockburn, Darrell

    AU - Wilkens, Casper

    AU - Ruzanski, Christian

    AU - Andersen, Susan

    AU - Willum Nielsen, Jonas

    AU - Smith, Alison M.

    AU - Field, Robert A.

    AU - Willemoes, Martin

    AU - Abou Hachem, Maher

    AU - Svensson, Birte

    PY - 2014

    Y1 - 2014

    N2 - Surface binding sites (SBSs) interact with carbohydrates outside of the enzyme active site. They are frequently situated on catalytic domains and are distinct from carbohydrate binding modules (CBMs). SBSs are found in a variety of enzymes and often seen in crystal structures. Notably about half of the > 45 enzymes (in 17 GH and two GT families) with an identified SBS are from GH13 and a few from GH77, both belonging to clan GH-H of carbohydrate active enzymes. The many enzymes of GH13 with SBSs provide an opportunity to analyse their distribution within this very large and diverse family. SBS containing enzymes in GH13 are spread among 15 subfamilies (two were not assigned a subfamily). Comparison of these SBSs reveals a complex evolutionary history with evidence of conservation of key residues and/or structural location between some SBSs, while others are found at entirely distinct structural locations, suggesting convergent evolution. An array of investigations of the two SBSs in barley α-amylase demonstrated they play different functional roles in binding and degradation of polysaccharides. MalQ from Escherichia coli is an α-1,4-glucanotransferase of GH77, a family that is known to have at least one member that contains an SBS. Whereas MalQ is a single domain enzyme lacking CBMs, its plant orthologue DPE2 contains two N-terminal CBM20s. Surface plasmon resonance binding studies showed that MalQ and DPE2 have a similar affinity for β-cyclodextrin and that MalQ binds malto-oligosaccharides of >DP4 at a second site in competition with β-cyclodextrin yielding a stoichiometry >1. This suggests that MalQ may have an SBS, though its structural location remains unknown.

    AB - Surface binding sites (SBSs) interact with carbohydrates outside of the enzyme active site. They are frequently situated on catalytic domains and are distinct from carbohydrate binding modules (CBMs). SBSs are found in a variety of enzymes and often seen in crystal structures. Notably about half of the > 45 enzymes (in 17 GH and two GT families) with an identified SBS are from GH13 and a few from GH77, both belonging to clan GH-H of carbohydrate active enzymes. The many enzymes of GH13 with SBSs provide an opportunity to analyse their distribution within this very large and diverse family. SBS containing enzymes in GH13 are spread among 15 subfamilies (two were not assigned a subfamily). Comparison of these SBSs reveals a complex evolutionary history with evidence of conservation of key residues and/or structural location between some SBSs, while others are found at entirely distinct structural locations, suggesting convergent evolution. An array of investigations of the two SBSs in barley α-amylase demonstrated they play different functional roles in binding and degradation of polysaccharides. MalQ from Escherichia coli is an α-1,4-glucanotransferase of GH77, a family that is known to have at least one member that contains an SBS. Whereas MalQ is a single domain enzyme lacking CBMs, its plant orthologue DPE2 contains two N-terminal CBM20s. Surface plasmon resonance binding studies showed that MalQ and DPE2 have a similar affinity for β-cyclodextrin and that MalQ binds malto-oligosaccharides of >DP4 at a second site in competition with β-cyclodextrin yielding a stoichiometry >1. This suggests that MalQ may have an SBS, though its structural location remains unknown.

    KW - HASH(0x53dca48)

    KW - Secondary binding sites

    KW - Carbohydrate binding modules

    KW - GH13 subfamilies

    KW - Crystal structures

    KW - Surface plasmon resonance

    KW - Affinity gel electrophoresis

    KW - Amylopectin hydrolysis kinetics

    U2 - 10.2478/s11756-014-0373-9

    DO - 10.2478/s11756-014-0373-9

    M3 - Journal article

    VL - 69

    SP - 705

    EP - 712

    JO - Biologia

    JF - Biologia

    SN - 0006-3088

    IS - 6

    ER -