Crystal structure and substrate-binding mode of a novel pectate lyase from alkaliphilic Bacillus sp N16-5

被引：36

作者：

Zheng, Yingying ^{[1
]}

Huang, Chun-Hsiang ^{[1
]}

Liu, Wenting ^{[1
,2
]}

Ko, Tzu-Ping ^{[3
]}

Xue, Yanfen ^{[4
]}

Zhou, Cheng ^{[4
]}

Guo, Rey-Ting ^{[1
]}

Ma, Yanhe ^{[1
,4
]}

机构：

[1] Chinese Acad Sci, Ind Enzymes Natl Engn Lab, Tianjin Inst Ind Biotechnol, Tianjin 300308, Peoples R China

[2] Tianjin Univ Sci & Technol, Tianjin 300457, Peoples R China

[3] Acad Sinica, Inst Biol Chem, Taipei 115, Taiwan

[4] Chinese Acad Sci, State Key Lab Microbial Resources, Inst Microbiol, Beijing 100101, Peoples R China

来源：

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS | 2012年 / 420卷 / 02期

关键词：

Pectin; Pectate lyase; Trigalacturonate; Ca2+ binding; Crystal structure; REFINED 3-DIMENSIONAL STRUCTURE; ERWINIA-CHRYSANTHEMI; SEQUENCE ALIGNMENT; SOFTWARE; PROTEINS; RESOLUTION; MECHANISM; TOOLS; FOLDS;

D O I：

10.1016/j.bbrc.2012.02.148

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The pectate lyase (Bsp165PelA) from Bacillus sp. N16-5 has great potential in industrial applications because it shows high specific activity under extremely alkaline conditions. Besides, activity measurement of Bsp165PelA does not require addition of calcium, in a way different from the other pectate lyases. Here we report crystal structures of Bsp165PelA in apo-form and in complex with trigalacturonate. The parallel beta-helix, active site residues and substrate binding cleft are similar to those in the other pectate lyases from Polysaccharide Lyase family 1. However, some of the highly conserved Ca2+ binding residues and secondary structures are altered in Bsp165PelA, making it difficult to coordinate with Ca2+ as in the other pectate lyases. We found Bsp165PelA forms some direct enzyme-substrate interactions instead of using Ca2+ ions bridging in the extremely alkaline environment. (C) 2012 Elsevier Inc. All rights reserved.

引用

页码：269 / 274

页数：6

共 28 条

[1] PHENIX:: building new software for automated crystallographic structure determination [J].

Adams, PD ;

Grosse-Kunstleve, RW ;

Hung, LW ;

Ioerger, TR ;

McCoy, AJ ;

Moriarty, NW ;

Read, RJ ;

Sacchettini, JC ;

Sauter, NK ;

Terwilliger, TC .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2002, 58 :1948-1954

[2] The first structure of pectate lyase belonging to polysaccharide lyase family 3 [J].

Akita, M ;

Suzuki, A ;

Kobayashi, T ;

Ito, S ;

Yamane, T .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2001, 57 :1786-1792

[3] ASSESSMENT OF PHASE ACCURACY BY CROSS VALIDATION - THE FREE R-VALUE - METHODS AND APPLICATIONS [J].

BRUNGER, AT .

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1993, 49 :24-36

[4] Crystallography & NMR system:: A new software suite for macromolecular structure determination [J].

Brunger, AT ;

Adams, PD ;

Clore, GM ;

DeLano, WL ;

Gros, P ;

Grosse-Kunstleve, RW ;

Jiang, JS ;

Kuszewski, J ;

Nilges, M ;

Pannu, NS ;

Read, RJ ;

Rice, LM ;

Simonson, T ;

Warren, GL .

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1998, 54 :905-921

[5] Crystal structure of Jun a 1, the major cedar pollen allergen from Juniperus ashei, reveals a parallel β-helical core [J].

Czerwinski, EW ;

Midoro-Horiuti, T ;

White, MA ;

Brooks, EG ;

Goldblum, RM .

JOURNAL OF BIOLOGICAL CHEMISTRY, 2005, 280 (05) :3740-3746

[6] Coot:: model-building tools for molecular graphics [J].

Emsley, P ;

Cowtan, K .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2004, 60 :2126-2132

[7] ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins [J].

Gouet, P ;

Robert, X ;

Courcelle, E .

NUCLEIC ACIDS RESEARCH, 2003, 31 (13) :3320-3323

[8] STRUCTURE-BASED MULTIPLE ALIGNMENT OF EXTRACELLULAR PECTATE LYASE SEQUENCES [J].

HEFFRON, S ;

HENRISSAT, B ;

YODER, MD ;

LIETZKE, S ;

JURNAK, F .

MOLECULAR PLANT-MICROBE INTERACTIONS, 1995, 8 (02) :331-334

[9] FUNCTIONAL IMPLICATIONS OF STRUCTURE-BASED SEQUENCE ALIGNMENT OF PROTEINS IN THE EXTRACELLULAR PECTATE LYASE SUPERFAMILY [J].

HENRISSAT, B ;

HEFFRON, SE ;

YODER, MD ;

LIETZKE, SE ;

JURNAK, F .

PLANT PHYSIOLOGY, 1995, 107 (03) :963-976

[10] Structure and function of pectic enzymes: Virulence factors of plant pathogens [J].

Herron, SR ;

Benen, JAE ;

Scavetta, RD ;

Visser, J ;

Jurnak, F .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (16) :8762-8769

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