Atomic structure of Mycobacterium tuberculosis CYP121 to 1.06 A reveals novel features of cytochrome P450

D Leys; CG Mowat; KJ McLean; A Richmond; SK Chapman; MD Walkinshaw; AW Munro

doi:10.1074/jbc.M209928200

Atomic structure of Mycobacterium tuberculosis CYP121 to 1.06 A reveals novel features of cytochrome P450

D Leys^*, CG Mowat, KJ McLean, A Richmond, SK Chapman, MD Walkinshaw, AW Munro

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

133 Citations (Scopus)

Abstract

The first structure of a P450 to an atomic resolution of 1.06 Angstrom has been solved for CYP121 from Mycobacterium tuberculosis. A comparison with P450 EryF (CYP107A1) reveals a remarkable overall similarity in fold with major differences residing in active site structural elements. The high resolution obtained allows visualization of several unusual aspects. The heme cofactor is bound in two distinct conformations while being notably kinked in one pyrrole group due to close interaction with the proline residue (Pro(346)) immediately following the heme iron-ligating cysteine (Cys(345)). The active site is remarkably rigid in comparison with the remainder of the structure, notwithstanding the large cavity volume of 1350 Angstrom(3). The region immediately surrounding the distal water ligand is remarkable in several aspects. Unlike other bacterial P450s, the I helix shows no deformation, similar to mammalian CYP2C5. In addition, the positively charged Arg(386) is located immediately above the heme plane, dominating the local structure. Putative proton relay pathways from protein surface to heme (converging at Ser(279)) are identified. Most interestingly, the electron density indicates weak binding of a dioxygen molecule to the P450. This structure provides a basis for rational design of putative antimycobacterial agents.

Original language	English
Pages (from-to)	5141-5147
Number of pages	7
Journal	Journal of Biological Chemistry
Volume	278
Issue number	7
DOIs	https://doi.org/10.1074/jbc.M209928200
Publication status	Published - 14 Feb 2003

Bibliographical note

Acknowledgments
We are grateful to Prof. Stewart Cole (Institut Pasteur, Paris) for provision of cosmid DNA and for helpful scientific discussions. We gratefully acknowledge beamtime received at Synchrotron Radiation Source (Daresbury, UK), European Synchrotron Radiation Facility (Grenoble, France), and EMBL X11 beamline at the DORIS storage ring, Deutsches Electronen-Synchrotron (Hamburg, Germany).

Keywords

CRYSTAL-STRUCTURE
ACTIVE-SITE
HEMOPROTEIN DOMAIN
HEME DOMAIN
SUBSTRATE
SUPERFAMILY
REFINEMENT
PROTOTYPE
ENZYMES
BINDING

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1074/jbc.M209928200

Cite this

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title = "Atomic structure of Mycobacterium tuberculosis CYP121 to 1.06 A reveals novel features of cytochrome P450",

abstract = "The first structure of a P450 to an atomic resolution of 1.06 Angstrom has been solved for CYP121 from Mycobacterium tuberculosis. A comparison with P450 EryF (CYP107A1) reveals a remarkable overall similarity in fold with major differences residing in active site structural elements. The high resolution obtained allows visualization of several unusual aspects. The heme cofactor is bound in two distinct conformations while being notably kinked in one pyrrole group due to close interaction with the proline residue (Pro(346)) immediately following the heme iron-ligating cysteine (Cys(345)). The active site is remarkably rigid in comparison with the remainder of the structure, notwithstanding the large cavity volume of 1350 Angstrom(3). The region immediately surrounding the distal water ligand is remarkable in several aspects. Unlike other bacterial P450s, the I helix shows no deformation, similar to mammalian CYP2C5. In addition, the positively charged Arg(386) is located immediately above the heme plane, dominating the local structure. Putative proton relay pathways from protein surface to heme (converging at Ser(279)) are identified. Most interestingly, the electron density indicates weak binding of a dioxygen molecule to the P450. This structure provides a basis for rational design of putative antimycobacterial agents.",

keywords = "CRYSTAL-STRUCTURE, ACTIVE-SITE, HEMOPROTEIN DOMAIN, HEME DOMAIN, SUBSTRATE, SUPERFAMILY, REFINEMENT, PROTOTYPE, ENZYMES, BINDING",

author = "D Leys and CG Mowat and KJ McLean and A Richmond and SK Chapman and MD Walkinshaw and AW Munro",

note = "Acknowledgments We are grateful to Prof. Stewart Cole (Institut Pasteur, Paris) for provision of cosmid DNA and for helpful scientific discussions. We gratefully acknowledge beamtime received at Synchrotron Radiation Source (Daresbury, UK), European Synchrotron Radiation Facility (Grenoble, France), and EMBL X11 beamline at the DORIS storage ring, Deutsches Electronen-Synchrotron (Hamburg, Germany).",

year = "2003",

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doi = "10.1074/jbc.M209928200",

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T1 - Atomic structure of Mycobacterium tuberculosis CYP121 to 1.06 A reveals novel features of cytochrome P450

AU - Leys, D

AU - Mowat, CG

AU - McLean, KJ

AU - Richmond, A

AU - Chapman, SK

AU - Walkinshaw, MD

AU - Munro, AW

N1 - Acknowledgments We are grateful to Prof. Stewart Cole (Institut Pasteur, Paris) for provision of cosmid DNA and for helpful scientific discussions. We gratefully acknowledge beamtime received at Synchrotron Radiation Source (Daresbury, UK), European Synchrotron Radiation Facility (Grenoble, France), and EMBL X11 beamline at the DORIS storage ring, Deutsches Electronen-Synchrotron (Hamburg, Germany).

PY - 2003/2/14

Y1 - 2003/2/14

N2 - The first structure of a P450 to an atomic resolution of 1.06 Angstrom has been solved for CYP121 from Mycobacterium tuberculosis. A comparison with P450 EryF (CYP107A1) reveals a remarkable overall similarity in fold with major differences residing in active site structural elements. The high resolution obtained allows visualization of several unusual aspects. The heme cofactor is bound in two distinct conformations while being notably kinked in one pyrrole group due to close interaction with the proline residue (Pro(346)) immediately following the heme iron-ligating cysteine (Cys(345)). The active site is remarkably rigid in comparison with the remainder of the structure, notwithstanding the large cavity volume of 1350 Angstrom(3). The region immediately surrounding the distal water ligand is remarkable in several aspects. Unlike other bacterial P450s, the I helix shows no deformation, similar to mammalian CYP2C5. In addition, the positively charged Arg(386) is located immediately above the heme plane, dominating the local structure. Putative proton relay pathways from protein surface to heme (converging at Ser(279)) are identified. Most interestingly, the electron density indicates weak binding of a dioxygen molecule to the P450. This structure provides a basis for rational design of putative antimycobacterial agents.

AB - The first structure of a P450 to an atomic resolution of 1.06 Angstrom has been solved for CYP121 from Mycobacterium tuberculosis. A comparison with P450 EryF (CYP107A1) reveals a remarkable overall similarity in fold with major differences residing in active site structural elements. The high resolution obtained allows visualization of several unusual aspects. The heme cofactor is bound in two distinct conformations while being notably kinked in one pyrrole group due to close interaction with the proline residue (Pro(346)) immediately following the heme iron-ligating cysteine (Cys(345)). The active site is remarkably rigid in comparison with the remainder of the structure, notwithstanding the large cavity volume of 1350 Angstrom(3). The region immediately surrounding the distal water ligand is remarkable in several aspects. Unlike other bacterial P450s, the I helix shows no deformation, similar to mammalian CYP2C5. In addition, the positively charged Arg(386) is located immediately above the heme plane, dominating the local structure. Putative proton relay pathways from protein surface to heme (converging at Ser(279)) are identified. Most interestingly, the electron density indicates weak binding of a dioxygen molecule to the P450. This structure provides a basis for rational design of putative antimycobacterial agents.

KW - CRYSTAL-STRUCTURE

KW - ACTIVE-SITE

KW - HEMOPROTEIN DOMAIN

KW - HEME DOMAIN

KW - SUBSTRATE

KW - SUPERFAMILY

KW - REFINEMENT

KW - PROTOTYPE

KW - ENZYMES

KW - BINDING

U2 - 10.1074/jbc.M209928200

DO - 10.1074/jbc.M209928200

M3 - Article

SN - 0021-9258

VL - 278

SP - 5141

EP - 5147

JO - Journal of Biological Chemistry

JF - Journal of Biological Chemistry

IS - 7

ER -

Atomic structure of Mycobacterium tuberculosis CYP121 to 1.06 A reveals novel features of cytochrome P450

Abstract

Bibliographical note

Keywords

UN SDGs

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