Topological comparison of adenyl kinase with other proteins

A COMBINATION of amino acid sequence analysis1 and X-ray analysis has yielded the atomic structure of the enzyme adenyl kinase2 (adenylate kinase, EC 2.7.4.3). No protein of which the structure is known is so closely related to adenyl kinase that an amino acid sequence comparison3 or an exact geometrical comparison of the structures4–6 can be expected to indicate a relationship. Similarities with other proteins become apparent, however, if one restricts the comparison to topologies, that is, to chain folds without reference to the exact geometry. Since chain folds are particularly well conserved during evolution7 such a procedure might reveal distant relationships.

[1]  D. Moras,et al.  D-glyceraldehyde-3-phosphate dehydrogenase: three-dimensional structure and evolutionary significance. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[2]  L. Sieker,et al.  Structure of the oxidized form of a flavodoxin at 2.5-Angstrom resolution: resolution of the phase ambiguity by anomalous scattering. , 1972, Proceedings of the National Academy of Sciences of the United States of America.

[3]  I. von Zabern,et al.  The amino-acid sequence of sarcine adenylate kinase from skeletal muscle. , 1974, European journal of biochemistry.

[4]  R. Dickerson,et al.  Recurrence of the cytochrome fold in a nitrate-respiring bacterium. , 1973, Journal of molecular biology.

[5]  M G Rossmann,et al.  Comparison of super-secondary structures in proteins. , 1973, Journal of molecular biology.

[6]  J. Kraut,et al.  Structure of Subtilisin BPN′ at 2.5 Å Resolution , 1969, Nature.

[7]  J. Kraut,et al.  The aromatic substrate binding site in subtilisin BPN' and its resemblance to chymotrypsin. , 1972, Cold Spring Harbor symposia on quantitative biology.

[8]  P R Evans,et al.  Structure of horse muscle phosphoglycerate kinase. Some results on the chain conformation, substrate binding and evolution of the molecule from a 3 angstrom Fourier map. , 1974, Journal of molecular biology.

[9]  Hans Eklund,et al.  Structure of Liver Alcohol Dehydrogenase at 2.9-Å Resolution , 1973 .

[10]  Anders Liljas,et al.  Recognition of structural domains in globular proteins , 1974 .

[11]  M. Rossmann,et al.  Structural constraints of possible mechanisms of lactate dehydrogenase as shown by high resolution studies of the apoenzyme and a variety of enzyme complexes. , 1972, Cold Spring Harbor symposia on quantitative biology.

[12]  R. M. Burnett,et al.  Structure of the radical form of clostridial flavodoxin: a new molecular model. , 1972, Proceedings of the National Academy of Sciences of the United States of America.

[13]  A. Mclachlan.  Gene duplication in carp muscle calcium binding protein. , 1972, Nature: New biology.

[14]  M. O. Dayhoff,et al.  Atlas of protein sequence and structure , 1965 .

[15]  J. Drenth,et al.  A comparison of the three-dimensional structures of subtilisin BPN' and subtilisin novo. , 1972, Cold Spring Harbor symposia on quantitative biology.

[16]  D. Wetlaufer.  Nucleation, rapid folding, and globular intrachain regions in proteins. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Leonard J. Banaszak,et al.  Polypeptide conformation of cytoplasmic malate dehydrogenase from an electron density map at 3.0 Å resolution , 1972 .

[18]  G. Schulz,et al.  Three-dimensional structure of adenyl kinase , 1974, Nature.