1HV6 | pdb_00001hv6

CRYSTAL STRUCTURE OF ALGINATE LYASE A1-III COMPLEXED WITH TRISACCHARIDE PRODUCT.

• PDB DOI: https://doi.org/10.2210/pdb1HV6/pdb

• Classification: LYASE
• Organism(s): Sphingomonas sp.
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 2001-01-08 Released: 2001-05-02 
• Deposition Author(s): Yoon, H.-J., Hashimoto, W., Miyake, O., Murata, K., Mikami, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.197 (Depositor) 
• R-Value Work: 
  0.158 (Depositor) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of alginate lyase A1-III complexed with trisaccharide product at 2.0 A resolution.

Yoon, H.J., Hashimoto, W., Miyake, O., Murata, K., Mikami, B.

(2001) J Mol Biology 307: 9-16

• PubMed: 11243798 
• DOI: https://doi.org/10.1006/jmbi.2000.4509
• Primary Citation Related Structures: 
  1HV6


• PubMed Abstract: 
  

  The structure of A1-III from a Sphingomonas species A1 complexed with a trisaccharide product (4-deoxy-l-erythro-hex-4-enepyranosyluronate-mannuronate-mannuronic acid) was determined by X-ray crystallography at 2.0 A with an R-factor of 0.16. The final model of the complex form comprising 351 amino acid residues, 245 water molecules, one sulfate ion and one trisaccharide product exhibited a C(alpha) r.m.s.d. value of 0.154 A with the reported apo form of the enzyme. The trisaccharide was bound in the active cleft at subsites -3 approximately -1 from the non-reducing end by forming several hydrogen bonds and van der Waals interactions with protein atoms. The catalytic residue was estimated to be Tyr246, which existed between subsites -1 and +1 based on a mannuronic acid model oriented at subsite +1.

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Organizational Affiliation: 
• Research Institute for Food Science, Kyoto University, Uji Kyoto 611-0011, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 40.27 kDa 
• Atom Count: 3,079 
• Modeled Residue Count: 351 
• Deposited Residue Count: 351 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALGINATE LYASE	A	351	Sphingomonas sp.	Mutation(s): 0  EC: 4.2.2.3
UniProt
Find proteins for A0ACD6B938 (Sphingomonas sp) Explore A0ACD6B938  Go to UniProtKB:  A0ACD6B938

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid-(1-4)-alpha-D-glucopyranuronic acid	B	3		N/A
Glycosylation Resources
GlyTouCan: G62159RG GlyCosmos: G62159RG

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.197 (Depositor) 
• R-Value Work:  0.158 (Depositor) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.765	α = 90
b = 92.92	β = 104.11
c = 82.22	γ = 90

Software Package:

Software Name	Purpose
SADIE/SAINT	data collection
SAINT	data reduction
CNS	refinement
SADIE	data reduction
SAINT	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-05-02 
Deposition Author(s): Yoon, H.-J., Hashimoto, W., Miyake, O., Murata, K., Mikami, B.

Revision History  

• Version 1.0: 2001-05-02
  Type: Initial release
  
• Version 1.1: 2008-04-27
  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, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary