EC Classification The EC Classification

EC Classification The EC Classification www.phwiki.com

EC Classification The EC Classification

Armstrong, Michael, On-Air Personality has reference to this Academic Journal, PHwiki organized this Journal Adventures in Computational Enzymology John Mitchell Mechanism, Annotation in addition to Classification in Enzymes. http://www.ebi.ac.uk/thornton-srv/databases/MACiE/ MACiE Database G.L. Holliday et al., Nucl. Acids Res., 35, D515-D520 (2007) Enzyme Nomenclature in addition to Classification

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EC Classification Enzyme Commission (EC) Nomenclature, 1992, Academic Press, San Diego, 6th Edition Chemical reaction The EC Classification Reaction direction arbitrary. Doesn’t deal with structural in addition to sequence in as long as mation. Thus, cofactors in addition to active site residues ignored. However, it was never intended to describe mechanism. Only deals with overall reaction. A New Representation of Enzyme Reactions Should be complementary to, but distinct from, the EC system. Should take into account: Reaction Mechanism; Structure; Sequence. Need a database of enzyme mechanisms.

Mechanism, Annotation in addition to Classification in Enzymes. http://www.ebi.ac.uk/thornton-srv/databases/MACiE/ MACiE Database Coverage of MACiE Representative – based on a non-homologous dataset, in addition to chosen to represent each available EC sub-subclass. Coverage of MACiE Representative – based on a non-homologous dataset, in addition to chosen to represent each available EC sub-subclass. Structures exist as long as : 6 EC 1.-.-.- 56 EC 1.2.-.- 184 EC 1.2.3.- 1312 EC 1.2.3.4 MACiE covers: 6 EC 1.-.-.- 53 EC 1.2.-.- 156 EC 1.2.3.- 199 EC 1.2.3.4

Repertoire of Enzyme Catalysis G.L. Holliday et al., J. Molec. Biol., 372, 1261-1277 (2007) Repertoire of Enzyme Catalysis Enzyme chemistry is largely nucleophilic Repertoire of Enzyme Catalysis

Residue Catalytic Propensities Evolution of Enzyme Function D.E. Almonacid et al., to be published Work with domains – evolutionary & structural units of proteins. Map enzyme catalytic mechanisms to domains to quantify convergent in addition to divergent functional evolution of enzymes. Domains

Functional Classification: EC Enzyme Commission (EC) Nomenclature, 1992, Academic Press, San Diego, 6th Edition Chemical reaction Enzyme Catalysis Databases G.L. Holliday et al., Nucleic Acids Res., 35, D515 (2007) S.C. Pegg et al., Biochemistry, 45, 2545 (2006) N. Nagano, Nucleic Acids Res., 33, D407 (2005) Coverage of MACiE Representative – based on a non-homologous dataset, in addition to chosen to represent each available EC sub-subclass.

Coverage of SFLD Based on a few evolutionarily related families Coverage of EzCatDB But without mechanisms. Structural Classification: CATH Orengo, C. A., et al. Structure, 1997, 5, 1093

Dataset CATH Enzymes in (single-domain) PDB Database entries 395 >>799 EC sub-subclasses 114 184 EC serial numbers 326 1312 To avoid the ambiguity of multi-domain structures we use only single-domain proteins. Numbers of CATH code occurrences per EC number C A T H c.-.-.- c.s.-.- c.s.ss.- c.s.ss.sn 3.17 11.00 28.00 38.33 1.73 3.27 4.89 5.80 1.38 1.93 2.24 2.46 1.11 1.60 1.19 1.22 Results: Convergent Evolution 2.46 CATH/EC reaction Convergent Evolution Numbers of CATH code occurrences per EC number C A T H c.-.-.- c.s.-.- c.s.ss.- c.s.ss.sn 3.17 11.00 28.00 38.33 1.73 3.27 4.89 5.80 1.38 1.93 2.24 2.46 1.11 1.60 1.19 1.22 Results: Convergent Evolution 2.46 CATH/EC reaction: Convergent Evolution An average reaction has evolved independently in 2.46 superfamilies

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EC reactions/CATH C 4.75 19.50 39.25 90.00 c.-.-.- c.s.-.- c.s.ss.- c.s.ss.sn A 3.14 7.00 10.48 17.90 T 1.36 1.79 2.08 3.05 H 1.20 1.36 1.46 2.05 database entries/CATH 2.18 Results: Divergent Evolution 1.46 EC reactions/CATH Divergent Evolution EC reactions/CATH C 4.75 19.50 39.25 90.00 c.-.-.- c.s.-.- c.s.ss.- c.s.ss.sn A 3.14 7.00 10.48 17.90 T 1.36 1.79 2.08 3.05 H 1.20 1.36 1.46 2.05 database entries/CATH 2.18 Results: Divergent Evolution 1.46 EC reactions/CATH: Divergent Evolution An average superfamily has evolved 1.46 different reactions Density Functional Theory Calculations on Dehydroquinase Mattias Blomberg et al., to be published

DFT – System Size System sizes of ~100-150 atoms can be treated using DFT That raises the question of how to treat the rest of the protein. Dielectric Continuum or QM/MM One approach is to cut out the active site residues in addition to treat the rest of the protein as a dielectric continuum. Another approach is to treat the active site as QM in addition to the rest of the protein using MM. QM =4 QM MM Dielectric Continuum or QM/MM One approach is to cut out the active site residues in addition to treat the rest of the protein as a dielectric continuum. Another approach is to treat the active site as QM in addition to the rest of the protein using MM. QM =4 QM MM

Residues Shown to Affect FosA Actvity in addition to Interactions with the Modelled GSH Most of the observed changes in FosA activity can be identified with the interactions with FCN or the modelled binding of GSH QM/MM-model of FosA Unrestricted Restricted Preliminary Energetics as long as FosA

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