4EIS | pdb_00004eis

Structural basis for substrate targeting and catalysis by fungal polysaccharide monooxygenases (PMO-3)

PDB DOI: https://doi.org/10.2210/pdb4EIS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Neurospora crassa OR74A
Mutation(s): No

Deposited: 2012-04-05 Released: 2012-05-23
Deposition Author(s): Li, X., Beeson, W.T., Phillips, C.M., Marletta, M.A., Cate, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.37 Å
R-Value Free:
0.149 (Depositor), 0.151 (DCC)
R-Value Work:
0.116 (Depositor), 0.121 (DCC)
R-Value Observed:
0.118 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Structural basis for substrate targeting and catalysis by fungal polysaccharide monooxygenases.

Li, X., Beeson, W.T., Phillips, C.M., Marletta, M.A., Cate, J.H.

(2012) Structure 20: 1051-1061

PubMed: 22578542 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.str.2012.04.002
Primary Citation Related Structures:
4EIR, 4EIS

PubMed Abstract:
The use of cellulases remains a major cost in the production of renewable fuels and chemicals from lignocellulosic biomass. Fungi secrete copper-dependent polysaccharide monooxygenases (PMOs) that oxidatively cleave crystalline cellulose and improve the effectiveness of cellulases. However, the means by which PMOs recognize and cleave their substrates in the plant cell wall remain unclear. Here, we present structures of Neurospora crassa PMO-2 and PMO-3 at 1.10 and 1.37 Å resolution, respectively. In the structures, dioxygen species are found in the active sites, consistent with the proposed cleavage mechanism. Structural and sequence comparisons between PMOs also reveal that the enzyme substrate-binding surfaces contain highly varied aromatic amino acid and glycosylation positions. The structures reported here provide evidence for a wide range of PMO substrate recognition patterns in the plant cell wall, including binding modes that traverse multiple glucan chains.

Organizational Affiliation

California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.

Macromolecule Content

Total Structure Weight: 49.55 kDa
Atom Count: 4,246
Modeled Residue Count: 450
Deposited Residue Count: 450
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
polysaccharide monooxygenase-3	A	225	Neurospora crassa OR74A	Mutation(s): 0 EC: 1.14.99.56
UniProt
Find proteins for Q7SA19 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)) Explore Q7SA19 Go to UniProtKB: Q7SA19
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7SA19
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
polysaccharide monooxygenase-3	B	225	Neurospora crassa OR74A	Mutation(s): 0 EC: 1.14.99.56
UniProt
Find proteins for Q7SA19 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)) Explore Q7SA19 Go to UniProtKB: Q7SA19
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7SA19
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
PER Query on PER Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PEROXIDE ION O₂ ANAIPYUSIMHBEL-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAH Query on DAH	A	L-PEPTIDE LINKING	C₉ H₁₁ N O₄		TYR
HIC Query on HIC	A	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.37 Å
R-Value Free: 0.149 (Depositor), 0.151 (DCC)
R-Value Work: 0.116 (Depositor), 0.121 (DCC)
R-Value Observed: 0.118 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.74	α = 90
b = 77.89	β = 90.02
c = 82.05	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASES	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-05-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-05-23
Type: Initial release
Version 1.1: 2012-06-27
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2025-03-26
Changes: Data collection, Database references, Structure summary