Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 166.52 kDa 
• Atom Count: 12799 
• Modelled Residue Count: 1399 
• Deposited Residue Count: 1420 
• Unique protein chains: 1

3WNO

D308A mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with cycloisomaltooctaose

• DOI: 10.2210/pdb3WNO/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus circulans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-12-10 Released: 2014-02-05 
• Deposition Author(s): Suzuki, N., Fujimoto, Z., Kim, Y.M., Momma, M., Kishine, N., Suzuki, R., Kobayashi, M., Kimura, A., Funane, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.195 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Literature

Structural elucidation of the cyclization mechanism of alpha-1,6-glucan by Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase.

Suzuki, N., Fujimoto, Z., Kim, Y.M., Momma, M., Kishine, N., Suzuki, R., Suzuki, S., Kitamura, S., Kobayashi, M., Kimura, A., Funane, K.

(2014) J Biol Chem 289: 12040-12051

• PubMed: 24616103 
• DOI: 10.1074/jbc.M114.547992
• Primary Citation of Related Structures:  
  3WNK, 3WNL, 3WNM, 3WNN, 3WNO


• PubMed Abstract: 
  

Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase belongs to the glycoside hydrolase family 66 and catalyzes an intramolecular transglucosylation reaction that produces cycloisomaltooligosaccharides from dextran. The crystal structure of the core fragment from Ser-39 to Met-738 of B. circulans T-3040 cycloisomaltooligosaccharide glucanotransferase, devoid of its N-terminal signal peptide and C-terminal nonconserved regions, was determined. The structural model contained one catalytic (β/α)8-barrel domain and three β-domains. Domain N with an immunoglobulin-like β-sandwich fold was attached to the N terminus; domain C with a Greek key β-sandwich fold was located at the C terminus, and a carbohydrate-binding module family 35 (CBM35) β-jellyroll domain B was inserted between the 7th β-strand and the 7th α-helix of the catalytic domain A. The structures of the inactive catalytic nucleophile mutant enzyme complexed with isomaltohexaose, isomaltoheptaose, isomaltooctaose, and cycloisomaltooctaose revealed that the ligands bound in the catalytic cleft and the sugar-binding site of CBM35. Of these, isomaltooctaose bound in the catalytic site extended to the second sugar-binding site of CBM35, which acted as subsite -8, representing the enzyme·substrate complex when the enzyme produces cycloisomaltooctaose. The isomaltoheptaose and cycloisomaltooctaose bound in the catalytic cleft with a circular structure around Met-310, representing the enzyme·product complex. These structures collectively indicated that CBM35 functions in determining the size of the product, causing the predominant production of cycloisomaltooctaose by the enzyme. The canonical sugar-binding site of CBM35 bound the mid-part of isomaltooligosaccharides, indicating that the original function involved substrate binding required for efficient catalysis.

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Related Citations: 

• Crystallization and preliminary X-ray crystallographic analysis of cycloisomaltooligosaccharide glucanotransferase from Bacillus circulans T-3040.
  Suzuki, N., Kim, Y.M., Momma, M., Fujimoto, Z., Kobayashi, M., Kimura, A., Funane, K.
  (2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 946

• Deletion analysis of regions at the C-terminal part of cycloisomaltooligosaccharide glucanotransferase from Bacillus circulans T-3040.
  Funane, K., Kawabata, Y., Suzuki, R., Kim, Y.M., Kang, H.K., Suzuki, N., Fujimoto, Z., Kimura, A., Kobayashi, M.
  (2011) Biochim Biophys Acta 1814: 428

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Organizational Affiliation: 

From the Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cycloisomaltooligosaccharide glucanotransferase	A, B	710	Bacillus circulans	Mutation(s): 1  Gene Names: cit EC: 2.4.1.248
Find proteins for P94286 (Bacillus circulans) Explore P94286  Go to UniProtKB:  P94286

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
Cyclooctakis-(1-6)-(alpha-D-glucopyranose)	C, D, E, F	8		N/A

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose	G	4		N/A

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	IA [auth B], V [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	AA [auth B],  BA [auth B],  CA [auth B],  DA [auth B],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  O [auth A],  P [auth A],  Y [auth B],  Z [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	EA [auth B],  FA [auth B],  GA [auth B],  HA [auth B],  Q [auth A],  R [auth A],  S [auth A],  T [auth A],  U [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	H [auth A], W [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	I [auth A], X [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.195 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.928	α = 90
b = 167.715	β = 90
c = 174.861	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-12-10 
• Released Date: 2014-02-05 
Deposition Author(s): Suzuki, N., Fujimoto, Z., Kim, Y.M., Momma, M., Kishine, N., Suzuki, R., Kobayashi, M., Kimura, A., Funane, K.

Revision History  

• Version 1.0: 2014-02-05
  Type: Initial release
  
• Version 1.1: 2015-03-04
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2020-06-24
  Changes: Advisory, Data collection, Database references, Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary