Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 60.29 kDa 
• Atom Count: 4699 
• Modelled Residue Count: 519 
• Deposited Residue Count: 526 
• Unique protein chains: 1

1JD0

CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN CARBONIC ANHYDRASE XII COMPLEXED WITH ACETAZOLAMIDE

• DOI: 10.2210/pdb1JD0/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-06-11 Released: 2001-08-17 
• Deposition Author(s): Whittington, D.A., Waheed, A., Ulmasov, B., Shah, G.N., Grubb, J.H., Sly, W.S., Christianson, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.207 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 

Literature

Crystal structure of the dimeric extracellular domain of human carbonic anhydrase XII, a bitopic membrane protein overexpressed in certain cancer tumor cells.

Whittington, D.A., Waheed, A., Ulmasov, B., Shah, G.N., Grubb, J.H., Sly, W.S., Christianson, D.W.

(2001) Proc Natl Acad Sci U S A 98: 9545-9550

• PubMed: 11493685 
• DOI: 10.1073/pnas.161301298
• Primary Citation of Related Structures:  
  1JCZ, 1JD0


• PubMed Abstract: 
  

Overexpression of the zinc enzyme carbonic anhydrase (CA; EC ) XII is observed in certain human cancers. This bitopic membrane protein contains an N-terminal extracellular catalytic domain, a membrane-spanning alpha-helix, and a small intracellular C-terminal domain. We have determined the three-dimensional structure of the extracellular catalytic domain of human CA XII by x-ray crystallographic methods at 1.55-A resolution. The structure reveals a prototypical CA fold; however, two CA XII domains associate to form an isologous dimer, an observation that is confirmed by studies of the enzyme in solution. The identification of signature GXXXG and GXXXS motifs in the transmembrane sequence that facilitate helix-helix association is additionally consistent with dimeric architecture. The dimer interface is situated so that the active site clefts of each monomer are clearly exposed on one face of the dimer, and the C termini are located together on the opposite face of the dimer to facilitate membrane interaction. The amino acid composition of the active-site cleft closely resembles that of the other CA isozymes in the immediate vicinity of the catalytic zinc ion, but differs in the region of the nearby alpha-helical "130's segment." The structure of the CA XII-acetazolamide complex is also reported at 1.50-A resolution, and prospects for the design of CA XII-specific inhibitors of possible chemotherapeutic value are discussed.

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Organizational Affiliation: 

Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBONIC ANHYDRASE XII	A, B	263	Homo sapiens	Mutation(s): 0  Gene Names: CA12 EC: 4.2.1.1
Find proteins for O43570 (Homo sapiens) Explore O43570  Go to UniProtKB:  O43570
NIH Common Fund Data Resources
PHAROS:  O43570 GTEx:  ENSG00000074410

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AZM	A, B	5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE C4 H6 N4 O3 S2 BZKPWHYZMXOIDC-UHFFFAOYSA-N
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
AZM	Ki:  2.5   nM  BindingDB
AZM	Ki:  5.800000190734863   nM  BindingDB
AZM	Ki:  3   nM  BindingDB
AZM	Kd:  133   nM  BindingDB
AZM	Ki:  5.599999904632568   nM  BindingDB
AZM	Ki:  0.800000011920929   nM  BindingDB
AZM	Ki:  5.699999809265137   nM  BindingDB
AZM	IC50:  88   nM  BindingDB
AZM	Kd:  130   nM  BindingDB
AZM	IC50:  440   nM  BindingDB
AZM	IC50:  61   nM  BindingDB
AZM	Kd:  25   nM  BindingDB
AZM	Kd:  26   nM  BindingDB
AZM	Ki:  5   nM  BindingDB
AZM	IC50:  60   nM  BindingDB
AZM	Kd:  330   nM  BindingDB
AZM	Ki:  25   nM  BindingDB
AZM	Ki:  6   nM  BindingDB
AZM	Ki :  5.699999809265137   nM  PDBBind
AZM	Ki:  250   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.207 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.875	α = 90
b = 45.08	β = 93.98
c = 85.232	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-06-11 
• Released Date: 2001-08-17 
Deposition Author(s): Whittington, D.A., Waheed, A., Ulmasov, B., Shah, G.N., Grubb, J.H., Sly, W.S., Christianson, D.W.

Revision History  

• Version 1.0: 2001-08-17
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model