1CXK | pdb_00001cxk

COMPLEX BETWEEN A MALTONONAOSE SUBSTRATE AND BACILLUS CIRCULANS STRAIN 251 CGTASE E257Q/D229N

• PDB DOI: https://doi.org/10.2210/pdb1CXK/pdb

• Classification: TRANSFERASE
• Organism(s): Niallia circulans
• Expression System: Bacillus subtilis
• Mutation(s): Yes 


• Deposited: 1999-02-24 Released: 1999-05-03 
• Deposition Author(s): Uitdehaag, J.C.M., Kalk, K.H., Dijkstra, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.210 (Depositor) 
• R-Value Work: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

X-ray structures along the reaction pathway of cyclodextrin glycosyltransferase elucidate catalysis in the alpha-amylase family.

Uitdehaag, J.C., Mosi, R., Kalk, K.H., van der Veen, B.A., Dijkhuizen, L., Withers, S.G., Dijkstra, B.W.

(1999) Nat Struct Biol 6: 432-436

• PubMed: 10331869 
• DOI: https://doi.org/10.1038/8235
• Primary Citation Related Structures: 
  1CXK, 1CXL


• PubMed Abstract: 
  

  Cyclodextrin glycosyltransferase (CGTase) is an enzyme of the alpha-amylase family, which uses a double displacement mechanism to process alpha-linked glucose polymers. We have determined two X-ray structures of CGTase complexes, one with an intact substrate at 2.1 A resolution, and the other with a covalently bound reaction intermediate at 1.8 A resolution. These structures give evidence for substrate distortion and the covalent character of the intermediate and for the first time show, in atomic detail, how catalysis in the alpha-amylase family proceeds by the concerted action of all active site residues.

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Organizational Affiliation: 
• BIOSON Research Institute, University of Groningen, The Netherlands.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 77.81 kDa 
• Atom Count: 6,112 
• Modeled Residue Count: 686 
• Deposited Residue Count: 686 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (CYCLODEXTRIN-GLYCOSYLTRANSFERASE)	A	686	Niallia circulans	Mutation(s): 2  EC: 2.4.1.19
UniProt
Find proteins for P43379 (Niallia circulans) Explore P43379  Go to UniProtKB:  P43379

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C	9		N/A
Glycosylation Resources
GlyTouCan: G96412PU GlyCosmos: G96412PU

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	D, E	4		N/A
Glycosylation Resources
GlyTouCan: G87171PZ GlyCosmos: G87171PZ GlyGen: G87171PZ

Small Molecules

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

Biologically Interesting Molecules (External Reference) 

2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide / Nutrient

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900010	D, E	alpha-maltotetraose	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.210 (Depositor) 
• R-Value Work:  0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.124	α = 90
b = 110.905	β = 90
c = 67.593	γ = 90

Software Package:

Software Name	Purpose
MADNESS	data collection
BIOMOL	data reduction
TNT	refinement
MADNESS	data reduction
BIOMOL	data scaling
TNT	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-05-03 
Deposition Author(s): Uitdehaag, J.C.M., Kalk, K.H., Dijkstra, B.W.

Revision History  

• Version 1.0: 1999-05-03
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2018-04-18
  Changes: Data collection
• Version 1.5: 2019-11-06
  Changes: 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
• Version 2.1: 2021-11-03
  Changes: Database references, Structure summary
• Version 2.2: 2023-08-09
  Changes: Data collection, Refinement description
• Version 2.3: 2024-11-13
  Changes: Structure summary