2AAA | pdb_00002aaa

CALCIUM BINDING IN ALPHA-AMYLASES: AN X-RAY DIFFRACTION STUDY AT 2.1 ANGSTROMS RESOLUTION OF TWO ENZYMES FROM ASPERGILLUS

• PDB DOI: https://doi.org/10.2210/pdb2AAA/pdb

• Classification: GLYCOSIDASE
• Organism(s): Aspergillus niger
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 1991-02-27 Released: 1993-07-15 
• Deposition Author(s): Brady, L., Brzozowski, A.M., Derewenda, Z., Dodson, E.J., Dodson, G.G., Tsianakas, K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Work: 
  0.112 (Depositor), 0.131 (DCC) 

Starting Model: experimental

Literature

Calcium binding in alpha-amylases: an X-ray diffraction study at 2.1-A resolution of two enzymes from Aspergillus.

Boel, E., Brady, L., Brzozowski, A.M., Derewenda, Z., Dodson, G.G., Jensen, V.J., Petersen, S.B., Swift, H., Thim, L., Woldike, H.F.

(1990) Biochemistry 29: 6244-6249

• PubMed: 2207069 
• DOI: https://doi.org/10.1021/bi00478a019
• Primary Citation Related Structures: 
  2AAA


• PubMed Abstract: 
  

  X-ray diffraction analysis (at 2.1-A resolution) of an acid alpha-amylase from Aspergillus niger allowed a detailed description of the stereochemistry of the calcium-binding sites. The primary site (which is essential in maintaining proper folding around the active site) contains a tightly bound Ca2+ with an unusually high number of eight ligands (O delta 1 and O delta 2 of Asp175, O delta of Asn121, main-chain carbonyl oxygens of Glu162 and Glu210, and three water molecules). A secondary binding site was identified at the bottom of the substrate binding cleft; it involves the residues presumed to play a catalytic role (Asp206 and Glu230). This explains the inhibitory effect of calcium observed at higher concentrations. Neutral Aspergillus oryzae (TAKA) alpha-amylase was also refined in a new crystal at 2.1-A resolution. The structure of this homologous (over 80%) enzyme and additional kinetic studies support all the structural conclusions regarding both calcium-binding sites.

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Organizational Affiliation: 
• Chemistry Department, University of York, Heslington, U.K.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 54.63 kDa 
• Atom Count: 4,134 
• Modeled Residue Count: 476 
• Deposited Residue Count: 476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha-amylase	A	476	Aspergillus niger	Mutation(s): 0  EC: 3.2.1.1
UniProt
Find proteins for P56271 (Aspergillus niger) Explore P56271  Go to UniProtKB:  P56271
Glycosylation
Glycosylation Sites: 4

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D [auth E], E [auth F]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	G [auth A], H [auth A], I [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Work:  0.112 (Depositor), 0.131 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.1	α = 90
b = 98.3	β = 90
c = 138	γ = 90

Software Package:

Software Name	Purpose
Servalcat	refinement
PDB-REDO	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 1993-07-15 
Deposition Author(s): Brady, L., Brzozowski, A.M., Derewenda, Z., Dodson, E.J., Dodson, G.G., Tsianakas, K.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 1993-07-15
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-09-17
  Changes: Other
• Version 1.4: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.5: 2024-11-20
  Changes: Structure summary
• Version 2.0: 2026-03-18
  Type: Coordinate replacement
  Reason: Sequence discrepancy
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Experimental preparation, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary