1LK9 | pdb_00001lk9

The Three-dimensional Structure of Alliinase from Garlic

PDB DOI: https://doi.org/10.2210/pdb1LK9/pdb

Classification: LYASE
Organism(s): Allium sativum
Mutation(s): No

Deposited: 2002-04-24 Released: 2002-12-11
Deposition Author(s): Kuettner, E.B., Hilgenfeld, R., Weiss, M.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free:
0.221 (Depositor)
R-Value Work:
0.193 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The active principle of garlic at atomic resolution

Kuettner, E.B., Hilgenfeld, R., Weiss, M.S.

(2002) J Biological Chem 277: 46402-46407

PubMed: 12235163 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M208669200
Primary Citation Related Structures:
1LK9

PubMed Abstract:
Despite the fact that many cultures around the world value and utilize garlic as a fundamental component of their cuisine as well as of their medicine cabinets, relatively little is known about the plant's protein configuration that is responsible for the specific properties of garlic. Here, we report the three-dimensional structure of the garlic enzyme alliinase at 1.5 A resolution. Alliinase constitutes the major protein component in garlic bulbs, and it is able to cleave carbon-sulfur bonds. The active enzyme is a pyridoxal-5'-phosphate-dependent homodimeric glycoprotein and belongs to the class I family of pyridoxal-5'-phosphate-dependent enzymes. In addition, it contains a novel epidermal growth factor-like domain that makes it unique among all pyridoxal-5'-phosphate-dependent enzymes.

Organizational Affiliation

Department of Structural Biology and Crystallography, Institute of Molecular Biotechnology, Beutenbergstrasse 11, D-07745 Jena, Germany.

Macromolecule Content

Total Structure Weight: 107.17 kDa
Atom Count: 7,996
Modeled Residue Count: 852
Deposited Residue Count: 896
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALLIIN LYASE	A, B	448	Allium sativum	Mutation(s): 0 EC: 4.4.1.4
UniProt
Find proteins for Q01594 (Allium sativum) Explore Q01594 Go to UniProtKB: Q01594
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q01594
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	4		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G18638YB GlyCosmos: G18638YB GlyGen: G18638YB

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	D, F	2		N-Glycosylation	Interactions Focus chain D Focus chain F Interactions & Density Focus chain D Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G80587NA GlyCosmos: G80587NA GlyGen: G80587NA

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain N [auth A] MOL2 format, chain W [auth B] MOL2 format, chain N [auth A] mmCIF format, chain W [auth B] mmCIF format, chain N [auth A]	N [auth A], W [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain W [auth B] Interactions & Density Focus chain N [auth A] Focus chain W [auth B]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A]	O [auth A], P [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain O [auth A] Focus chain P [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
DHA Query on DHA Download:Ideal Coordinates CCD File SDF format, chain X [auth B] MOL2 format, chain X [auth B] mmCIF format, chain X [auth B]	X [auth B]	2-AMINO-ACRYLIC ACID C₃ H₅ N O₂ UQBOJOOOTLPNST-UHFFFAOYSA-N		Interactions Focus chain X [auth B] Interactions & Density Focus chain X [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain M [auth A] MOL2 format, chain V [auth B] MOL2 format, chain M [auth A] mmCIF format, chain V [auth B] mmCIF format, chain M [auth A]	M [auth A], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth A] Focus chain V [auth B] Interactions & Density Focus chain M [auth A] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free: 0.221 (Depositor)
R-Value Work: 0.193 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.45	α = 90
b = 101.07	β = 90
c = 155.69	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
TRUNCATE	data reduction
MLPHARE	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2002-12-11

Deposition Author(s):

Kuettner, E.B.

Hilgenfeld, R.

Weiss, M.S.

Revision History (Full details and data files)

Version 1.0: 2002-12-11
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2025-03-26
Changes: Data collection, Database references, Structure summary