PDBsum entry 1jd0

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Lyase PDB id
Protein chain
260 a.a. *
AZM ×2
_ZN ×2
Waters ×504
* Residue conservation analysis

References listed in PDB file
Key reference
Title Crystal structure of the dimeric extracellular domain of human carbonic anhydrase XII, A bitopic membrane protein overexpressed in certain cancer tumor cells.
Authors D.A.Whittington, A.Waheed, B.Ulmasov, G.N.Shah, J.H.Grubb, W.S.Sly, D.W.Christianson.
Ref. Proc Natl Acad Sci U S A, 2001, 98, 9545-9550. [DOI no: 10.1073/pnas.161301298]
PubMed id 11493685
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.
Figure 3.
Fig. 3. Schematic drawing showing the CA XII dimer in the membrane; orientation is the same as that in Fig. 2. The extracellular CA domains (molecules A and B) are colored blue and green, respectively. Zinc ions appear as white spheres, disulfide linkages are yellow, and acetazolamide molecules appear as balls-and-sticks. The yellow transmembrane helices are modeled after the structure of the glycophorin A dimer reported by MacKenzie and colleagues (42): both CA XII and glycophorin A contain transmembrane GXXXG dimerization motifs (40, 41). The intracellular C-terminal domains appear as orange spheres. These domains contain potential phosphorylation sites but are currently of unknown structure. Note that membrane association orients the enzyme active sites toward the extracellular milieu, poised for catalysis.
Figure 4.
Fig. 4. The active site of the native CA XII structure showing the five-coordinate zinc ion. The zinc ion is colored cyan. Oxygen, nitrogen, and carbon atoms are red, blue, and gray, respectively. Hydrogen bonds are shown as dashed lines with distances labeled (Å). Average zinc-ligand distances are as follows: Zn2+-His-94, 2.0 Å; Zn2+-His-96, 2.1 Å; Zn2+-His-119, 2.1 Å; Zn2+-OH[2], 2.1 Å; Zn2+-acetate, 2.3 Å.
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