1SUS | pdb_00001sus

Crystal structure of alfalfa feruoyl coenzyme A 3-O-methyltransferase

PDB DOI: https://doi.org/10.2210/pdb1SUS/pdb

Classification: TRANSFERASE
Organism(s): Medicago sativa
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-03-26 Released: 2005-03-15
Deposition Author(s): Ferrer, J.-L., Zubieta, C., Dixon, R.A., Noel, J.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.289 (Depositor), 0.281 (DCC)
R-Value Work:
0.245 (Depositor), 0.234 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structures of Alfalfa Caffeoyl Coenzyme A 3-O-Methyltransferase

Ferrer, J.-L., Zubieta, C., Dixon, R.A., Noel, J.P.

(2005) Plant Physiol 137: 1009-1017

PubMed: 15734921 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1104/pp.104.048751
Primary Citation Related Structures:
1SUI, 1SUS

PubMed Abstract:
Caffeoyl coenzyme A 3-O-methyltransferases (CCoAOMTs) are S-adenosyl-l-methionine-dependent O-methyltransferases (OMTs) involved in lignin biosynthesis. Plant CCoAOMTs belong to a distinct family of OMTs, more closely related to the mammalian catechol OMTs than to other plant OMTs. The crystal structure of alfalfa (Medicago sativa) CCoAOMT in complex with the reaction products S-adenosine-l-homocysteine and feruloyl/sinapoyl CoAs presented here belong to a structurally and mechanistically distinct family of plant small molecule OMTs. These structures provide a new understanding of the substrate preferences and the catalytic mechanism accompanying CCoAOMT-mediated O-methylation of CoA-linked phenylpropanoid substrates.

Organizational Affiliation

Laboratoire de Cristallographie et Cristallogenèse des Protéines, Institut de Biologie Structurale, 38027 Grenoble cedex 1, France.

Macromolecule Content

Total Structure Weight: 114.81 kDa
Atom Count: 7,447
Modeled Residue Count: 908
Deposited Residue Count: 988
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caffeoyl-CoA O-methyltransferase	A, B, C, D	247	Medicago sativa	Mutation(s): 0 Gene Names: CCOMT EC: 2.1.1.104
UniProt
Find proteins for Q40313 (Medicago sativa) Explore Q40313 Go to UniProtKB: Q40313
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q40313
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SPF Query on SPF Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SINAPOYL COENZYME A C₃₂ H₄₄ N₇ O₂₀ P₃ S HJGDVDUGXUSOGA-ADTMLPBESA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], K [auth C], M [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], J [auth C], L [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.289 (Depositor), 0.281 (DCC)
R-Value Work: 0.245 (Depositor), 0.234 (DCC)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.854	α = 90
b = 136.486	β = 90
c = 332.778	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
MLPHARE	phasing
CNS	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-03-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-03-15
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Derived calculations