1RWG

Crystal structure of Arthrobacter aurescens chondroitin AC lyase in complex with chondroitin tetrasaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

High-resolution crystal structure of Arthrobacter aurescens chondroitin AC lyase: an enzyme-substrate complex defines the catalytic mechanism

Lunin, V.V.Li, Y.Linhardt, R.J.Miyazono, H.Kyogashima, M.Kaneko, T.Bell, A.W.Cygler, M.

(2004) J.Mol.Biol. 337: 367-386

  • DOI: 10.1016/j.jmb.2003.12.071
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chondroitin lyases (EC 4.2.2.4 and EC 4.2.2.5) are glycosaminoglycan-degrading enzymes that act as eliminases. Chondroitin lyase AC from Arthrobacter aurescens (ArthroAC) is known to act on chondroitin 4-sulfate and chondroitin 6-sulfate but not on d ...

    Chondroitin lyases (EC 4.2.2.4 and EC 4.2.2.5) are glycosaminoglycan-degrading enzymes that act as eliminases. Chondroitin lyase AC from Arthrobacter aurescens (ArthroAC) is known to act on chondroitin 4-sulfate and chondroitin 6-sulfate but not on dermatan sulfate. Like other chondroitin AC lyases, it is capable of cleaving hyaluronan. We have determined the three-dimensional crystal structure of ArthroAC in its native form as well as in complex with its substrates (chondroitin 4-sulfate tetrasaccharide, CS(tetra) and hyaluronan tetrasaccharide) at resolution varying from 1.25 A to 1.9A. The primary sequence of ArthroAC has not been previously determined but it was possible to determine the amino acid sequence of this enzyme from the high-resolution electron density maps and to confirm it by mass spectrometry. The enzyme-substrate complexes were obtained by soaking the substrate into the crystals for varying lengths of time (30 seconds to ten hours) and flash-cooling the crystals. The electron density map for crystals soaked in the substrate for as short as 30 seconds showed the substrate clearly and indicated that the ring of central glucuronic acid assumes a distorted boat conformation. This structure strongly supports the lytic mechanism where Tyr242 acts as a general base that abstracts the proton from the C5 position of glucuronic acid while Asn183 and His233 neutralize the charge on the glucuronate acidic group. Comparison of this structure with that of chondroitinase AC from Flavobacterium heparinum (FlavoAC) provides an explanation for the exolytic and endolytic mode of action of ArthroAC and FlavoAC, respectively.


    Organizational Affiliation

    Biotechnology Research Institute, National Research Council of Canada, and Montréal Joint Centre for Structural Biology, Montréal, Québec, 6100 Royalmount Ave., Montréal, Québec, Canada H4P 2R2.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
chondroitin AC lyase
A
757Paenarthrobacter aurescensMutation(s): 0 
Find proteins for P84141 (Paenarthrobacter aurescens)
Go to UniProtKB:  P84141
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GAD
Query on GAD

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A
2,6-ANHYDRO-3-DEOXY-D-ERYTHRO-HEX-2-ENONIC ACID
C6 H8 O5
GQECVRZDTXJRPX-IMJSIDKUSA-N
 Ligand Interaction
GCT
Query on GCT

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Download CCD File 
A
4,5-DIHYDROXY-TETRAHYDRO-PYRAN-2-CARBOXYLIC ACID
C6 H10 O5
YRPRHLNMFWDGSL-YUPRTTJUSA-N
 Ligand Interaction
ASG
Query on ASG

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A
2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE
C8 H15 N O9 S
WHCJUIFHMJFEFZ-UIAUGNHASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.136 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.683α = 90.00
b = 86.449β = 106.87
c = 80.566γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-05-09
    Type: Other
  • Version 1.4: 2018-01-31
    Type: Experimental preparation