Modelling of the lignin peroxidase LIII of Phlebia radiata: Use of a sequence template generated from a 3-D structure

Anna-Marja Hoffren (Corresponding Author), Markku Saloheimo, Pamela Thomas, John Overington, Mark Johnson, Jonathan Knowles, Tom Blundell

Research output: Contribution to journalArticleScientificpeer-review

3 Citations (Scopus)

Abstract

A model of the lignin peroxidase LIII of Phlebia radiata was constructed on the basis of the structure of cytochrome c peroxidase (CCP). Because of the low percentage of amino acid identity between the CCP and the lignin peroxidase LIII of Phlebia radiata, alignment of the sequences was based on the generation of a template from a knowledge of the 3-D structure of CCP and consensus sequences of lignin peroxidases. This approach gave an alignment in which all the insertions in the lignin peroxidase were placed at loop regions of CCP, with a 21.1% identity for these two proteins. The model was constructed using this alignment and the computer program COMPOSER, which assembles the model as a series of rigid fragments derived from CCP and other proteins. Manual intervention was required for some of the longer loop regions. The α-helices forming the structural framework, and especially the haem environment of CCP, are conserved in the LIII model and the core is close packed without holes. A possible site of the substrate oxidation at the haem edge of LIII is discussed.

Original languageEnglish
Pages (from-to)177 - 182
Number of pages6
JournalProtein Engineering
Volume6
Issue number2
DOIs
Publication statusPublished - 1993
MoE publication typeA1 Journal article-refereed

Fingerprint

Cytochrome-c Peroxidase
Lignin
Proteins
Heme
Sequence Alignment
Consensus Sequence
lignin peroxidase
Computer program listings
Software
Amino acids
Amino Acids
Oxidation
Substrates

Cite this

Hoffren, Anna-Marja ; Saloheimo, Markku ; Thomas, Pamela ; Overington, John ; Johnson, Mark ; Knowles, Jonathan ; Blundell, Tom. / Modelling of the lignin peroxidase LIII of Phlebia radiata : Use of a sequence template generated from a 3-D structure. In: Protein Engineering. 1993 ; Vol. 6, No. 2. pp. 177 - 182.
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abstract = "A model of the lignin peroxidase LIII of Phlebia radiata was constructed on the basis of the structure of cytochrome c peroxidase (CCP). Because of the low percentage of amino acid identity between the CCP and the lignin peroxidase LIII of Phlebia radiata, alignment of the sequences was based on the generation of a template from a knowledge of the 3-D structure of CCP and consensus sequences of lignin peroxidases. This approach gave an alignment in which all the insertions in the lignin peroxidase were placed at loop regions of CCP, with a 21.1{\%} identity for these two proteins. The model was constructed using this alignment and the computer program COMPOSER, which assembles the model as a series of rigid fragments derived from CCP and other proteins. Manual intervention was required for some of the longer loop regions. The α-helices forming the structural framework, and especially the haem environment of CCP, are conserved in the LIII model and the core is close packed without holes. A possible site of the substrate oxidation at the haem edge of LIII is discussed.",
author = "Anna-Marja Hoffren and Markku Saloheimo and Pamela Thomas and John Overington and Mark Johnson and Jonathan Knowles and Tom Blundell",
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Modelling of the lignin peroxidase LIII of Phlebia radiata : Use of a sequence template generated from a 3-D structure. / Hoffren, Anna-Marja (Corresponding Author); Saloheimo, Markku; Thomas, Pamela; Overington, John; Johnson, Mark; Knowles, Jonathan; Blundell, Tom.

In: Protein Engineering, Vol. 6, No. 2, 1993, p. 177 - 182.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Modelling of the lignin peroxidase LIII of Phlebia radiata

T2 - Use of a sequence template generated from a 3-D structure

AU - Hoffren, Anna-Marja

AU - Saloheimo, Markku

AU - Thomas, Pamela

AU - Overington, John

AU - Johnson, Mark

AU - Knowles, Jonathan

AU - Blundell, Tom

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AB - A model of the lignin peroxidase LIII of Phlebia radiata was constructed on the basis of the structure of cytochrome c peroxidase (CCP). Because of the low percentage of amino acid identity between the CCP and the lignin peroxidase LIII of Phlebia radiata, alignment of the sequences was based on the generation of a template from a knowledge of the 3-D structure of CCP and consensus sequences of lignin peroxidases. This approach gave an alignment in which all the insertions in the lignin peroxidase were placed at loop regions of CCP, with a 21.1% identity for these two proteins. The model was constructed using this alignment and the computer program COMPOSER, which assembles the model as a series of rigid fragments derived from CCP and other proteins. Manual intervention was required for some of the longer loop regions. The α-helices forming the structural framework, and especially the haem environment of CCP, are conserved in the LIII model and the core is close packed without holes. A possible site of the substrate oxidation at the haem edge of LIII is discussed.

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