1I6P | pdb_00001i6p

CRYSTAL STRUCTURE OF E. COLI BETA CARBONIC ANHYDRASE (ECCA)

• PDB DOI: https://doi.org/10.2210/pdb1I6P/pdb

• Classification: LYASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2001-03-02 Released: 2001-05-09 
• Deposition Author(s): Cronk, J.D., Endrizzi, J.A., Cronk, M.R., O'Neill, J.W., Zhang, K.Y.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.202 (Depositor) 
• R-Value Work: 
  0.176 (Depositor) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of E. coli beta-carbonic anhydrase, an enzyme with an unusual pH-dependent activity.

Cronk, J.D., Endrizzi, J.A., Cronk, M.R., O'neill, J.W., Zhang, K.Y.

(2001) Protein Sci 10: 911-922

• PubMed: 11316870 
• DOI: https://doi.org/10.1110/ps.46301
• Primary Citation Related Structures: 
  1I6O, 1I6P


• PubMed Abstract: 
  

  Carbonic anhydrases fall into three distinct evolutionary and structural classes: alpha, beta, and gamma. The beta-class carbonic anhydrases (beta-CAs) are widely distributed among higher plants, simple eukaryotes, eubacteria, and archaea. We have determined the crystal structure of ECCA, a beta-CA from Escherichia coli, to a resolution of 2.0 A. In agreement with the structure of the beta-CA from the chloroplast of the red alga Porphyridium purpureum, the active-site zinc in ECCA is tetrahedrally coordinated by the side chains of four conserved residues. These results confirm the observation of a unique pattern of zinc ligation in at least some beta-CAS: The absence of a water molecule in the inner coordination sphere is inconsistent with known mechanisms of CA activity. ECCA activity is highly pH-dependent in the physiological range, and its expression in yeast complements an oxygen-sensitive phenotype displayed by a beta-CA-deletion strain. The structural and biochemical characterizations of ECCA presented here and the comparisons with other beta-CA structures suggest that ECCA can adopt two distinct conformations displaying widely divergent catalytic rates.

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Organizational Affiliation: 
• Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 25.2 kDa 
• Atom Count: 1,778 
• Modeled Residue Count: 214 
• Deposited Residue Count: 220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBONIC ANHYDRASE	A	220	Escherichia coli	Mutation(s): 0  Gene Names: YADF EC: 4.2.1.1
UniProt
Find proteins for P61517 (Escherichia coli (strain K12)) Explore P61517  Go to UniProtKB:  P61517

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.202 (Depositor) 
• R-Value Work:  0.176 (Depositor) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.535	α = 90
b = 68.535	β = 90
c = 85.877	γ = 90

Software Package:

Software Name	Purpose
EPMR	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-05-09 
Deposition Author(s): Cronk, J.D., Endrizzi, J.A., Cronk, M.R., O'Neill, J.W., Zhang, K.Y.J.

Revision History  

• Version 1.0: 2001-05-09
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description