1EE6

CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.186 

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This is version 1.2 of the entry. See complete history. 


Literature

The first structure of pectate lyase belonging to polysaccharide lyase family 3.

Akita, M., Suzuki, A., Kobayashi, T., Ito, S., Yamane, T.

(2001) Acta Crystallogr D Biol Crystallogr 57: 1786-1792

  • DOI: 10.1107/s0907444901014482
  • Primary Citation of Related Structures:  
    1EE6

  • PubMed Abstract: 

    • The crystal structure of a highly alkaline low molecular weight pectate lyase (Pel-15) was determined at 1.5 A resolution by the multiple isomorphous replacement (MIR) method. This is the first pectate lyase structure from polysaccharide lyase family 3. The overall structure is a simple eight-turn right-handed parallel beta-helix domain with one long loop protruding from one side of the beta-helix ...

    The crystal structure of a highly alkaline low molecular weight pectate lyase (Pel-15) was determined at 1.5 A resolution by the multiple isomorphous replacement (MIR) method. This is the first pectate lyase structure from polysaccharide lyase family 3. The overall structure is a simple eight-turn right-handed parallel beta-helix domain with one long loop protruding from one side of the beta-helix. The low molecular weight of Pel-15 derives from the lack of N- and C-terminal extensions that are found in many beta-helix proteins. Although the structure has one calcium ion at pH 6.7, raising the pH to 9.5 results in the binding of an additional calcium ion. The common calcium ion found in both the pH 6.5 and 9.5 structures seems to stabilize both the beta-helix structure and the long protruding loop. The additional calcium ion found in the pH 9.5 structure alone may neutralize the acidic substrate. The region around the additional calcium ion is thought to bind to the substrate, as this region is rich in charged amino-acid residues which are required in catalysis.

    Organizational Affiliation: 

    Department of Biotechnology and Biomaterial Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan. h991401d@mbox.media.nagoya-u.ac.jp



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PECTATE LYASEA197Bacillus sp. KSM-P15Mutation(s): 0 
EC: 4.2.2.2
UniProt
Find proteins for Q9RHW0 (Bacillus sp)
Explore Q9RHW0 
Go to UniProtKB:  Q9RHW0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RHW0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.9α = 90
b = 60.5β = 90
c = 83γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance