3IN9 | pdb_00003in9

Crystal structure of heparin lyase I complexed with disaccharide heparin

• PDB DOI: https://doi.org/10.2210/pdb3IN9/pdb

• Classification: LYASE
• Organism(s): Bacteroides thetaiotaomicron
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-08-12 Released: 2009-09-29 
• Deposition Author(s): Han, Y.H., Ryu, K.S., Kim, H.Y., Jeon, Y.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.217 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.182 (DCC) 

Starting Model: experimental

Literature

Structural snapshots of heparin depolymerization by heparin lyase I

Han, Y.H., Garron, M.L., Kim, H.Y., Kim, W.S., Zhang, Z., Ryu, K.S., Shaya, D., Xiao, Z., Cheong, C., Kim, Y.S., Linhardt, R.J., Jeon, Y.H., Cygler, M.

(2009) J Biological Chem 284: 34019-34027

• PubMed: 19801541 
• DOI: https://doi.org/10.1074/jbc.M109.025338
• Primary Citation Related Structures: 
  3IKW, 3ILR, 3IMN, 3IN9, 3INA


• PubMed Abstract: 
  

  Heparin lyase I (heparinase I) specifically depolymerizes heparin, cleaving the glycosidic linkage next to iduronic acid. Here, we show the crystal structures of heparinase I from Bacteroides thetaiotaomicron at various stages of the reaction with heparin oligosaccharides before and just after cleavage and product disaccharide. The heparinase I structure is comprised of a beta-jellyroll domain harboring a long and deep substrate binding groove and an unusual thumb-resembling extension. This thumb, decorated with many basic residues, is of particular importance in activity especially on short heparin oligosaccharides. Unexpected structural similarity of the active site to that of heparinase II with an (alpha/alpha)(6) fold is observed. Mutational studies and kinetic analysis of this enzyme provide insights into the catalytic mechanism, the substrate recognition, and processivity.

---

Organizational Affiliation: 
• Magnetic Resonance Team, Korea Basic Science Institute, Ochang, Chungbuk 363-883, Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.03 kDa 
• Atom Count: 3,352 
• Modeled Residue Count: 373 
• Deposited Residue Count: 378 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heparin lyase I	A	378	Bacteroides thetaiotaomicron	Mutation(s): 0
UniProt
Find proteins for Q89YQ6 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q89YQ6  Go to UniProtKB:  Q89YQ6

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose	B, C	2		N/A
Glycosylation Resources
GlyTouCan: G01871HO GlyCosmos: G01871HO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900026	B, C	HEPARIN DISACCHARIDE I-S,	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.217 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.182 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.789	α = 90
b = 63.531	β = 115.47
c = 65.204	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-29 
Deposition Author(s): Han, Y.H., Ryu, K.S., Kim, H.Y., Jeon, Y.H.

Revision History  

• Version 1.0: 2009-09-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary