5X7G

Crystal Structure of Paenibacillus sp. 598K cycloisomaltooligosaccharide glucanotransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Isomaltooligosaccharide-binding structure ofPaenibacillussp. 598K cycloisomaltooligosaccharide glucanotransferase

Fujimoto, Z.Kishine, N.Suzuki, N.Suzuki, R.Mizushima, D.Momma, M.Kimura, K.Funane, K.

(2017) Biosci. Rep. 37: --

  • DOI: 10.1042/BSR20170253
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Paenibacillus sp. 598K cycloisomaltooligosaccharide glucanotransferase (CITase), a member of glycoside hydrolase family 66 (GH66), catalyses the intramolecular transglucosylation of dextran to produce CIs with seven or more degrees of polymerization. ...

    Paenibacillus sp. 598K cycloisomaltooligosaccharide glucanotransferase (CITase), a member of glycoside hydrolase family 66 (GH66), catalyses the intramolecular transglucosylation of dextran to produce CIs with seven or more degrees of polymerization. To clarify the cyclization reaction and product specificity of the enzyme, we determined the crystal structure of PsCITase. The core structure of PsCITase consists of four structural domains: a catalytic (β/α)8-domain and three β-domains. A family 35 carbohydrate-binding module (first CBM35 region of Paenibacillus sp. 598K CITase, (PsCBM35-1)) is inserted into and protrudes from the catalytic domain. The ligand complex structure of PsCITase prepared by soaking the crystal with cycloisomaltoheptaose yielded bound sugars at three sites: in the catalytic cleft, at the joint of the PsCBM35-1 domain and at the loop region of PsCBM35-1. In the catalytic site, soaked cycloisomaltoheptaose was observed as a linear isomaltoheptaose, presumably a hydrolysed product from cycloisomaltoheptaose by the enzyme and occupied subsites -7 to -1. Beyond subsite -7, three glucose moieties of another isomaltooiligosaccharide were observed, and these positions are considered to be distal subsites -13 to -11. The third binding site is the canonical sugar-binding site at the loop region of PsCBM35-1, where the soaked cycloisomaltoheptaose is bound. The structure indicated that the concave surface between the catalytic domain and PsCBM35-1 plays a guiding route for the long-chained substrate at the cyclization reaction.


    Related Citations: 
    • Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from Paenibacillus sp. 598K
      Suzuki, R.,Terasawa, K.,Kimura, K.,Fujimoto, Z.,Momma, M.,Kobayashi, M.,Kimura, A.,Funane, K.
      (2012) Biochim. Biophys. Acta 1824: 919


    Organizational Affiliation

    Advanced Analysis Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan zui@affrc.go.jp funane@affrc.go.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cycloisomaltooligosaccharide glucanotransferase
A
720Paenibacillus sp. 598KMutation(s): 0 
Gene Names: cit
Find proteins for G9MBW2 (Paenibacillus sp. 598K)
Go to UniProtKB:  G9MBW2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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

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A
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.174 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 113.680α = 90.00
b = 113.680β = 90.00
c = 121.635γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MAFFJapan25001A

Revision History 

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Data collection
  • Version 1.2: 2017-12-06
    Type: Database references
  • Version 1.3: 2018-05-02
    Type: Data collection, Database references