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CATH Superfamily 3.10.28.10

Homing endonucleases

The name of this superfamily has been modified since the most recent official CATH+ release (v4_2_0). At the point of the last release, this superfamily was named:

"
Homing endonucleases
".

Functional Families

Overview of the Structural Clusters (SC) and Functional Families within this CATH Superfamily. Clusters with a representative structure are represented by a filled circle.
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FunFam 21994: DNA polymerase (Alpha family)

There are 9 EC terms in this cluster

Please note: EC annotations are assigned to the full protein sequence rather than individual protein domains. Since a given protein can contain multiple domains, it is possible that some of the annotations below come from additional domains that occur in the same protein, but have been classified elsewhere in CATH.

Note: The search results have been sorted with the annotations that are found most frequently at the top of the list. The results can be filtered by typing text into the search box at the top of the table.

EC Term Annotations Evidence
DNA-directed DNA polymerase. [EC: 2.7.7.7]
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
  • Catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time.
  • Cannot initiate a chain de novo.
  • Requires a primer which may be DNA or RNA.
  • See also EC 2.7.7.49.
 70 A0A097QS26 A0A097QS26 A0A097QTD6 A0A097QTD6 A0A0S1XDG0 A0A0S1XDG0 A0A101ENU1 A0A101ENU1 A0A101F2U1 A0A101F2U1
(60 more...)
Ribonucleoside-diphosphate reductase. [EC: 1.17.4.1]
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin.
  • This enzyme is responsible for the de novo conversion of ribonucleoside diphosphates into deoxyribonucleoside diphosphates, which are essential for DNA synthesis and repair.
  • There are three types of this enzyme differing in their cofactors.
  • Class Ia enzymes contain a diferric-tyrosyl radical, class Ib enzymes contain a dimanganese-tyrosyl radical, and class II enzymes contain adenosylcobalamin.
  • In all cases the cofactors are involved in generation of a transient thiyl radical on a cysteine residue, which attacks the substrate, forming a ribonucleotide 3'-radical, followed by water loss to form a ketyl radical.
  • The ketyl radical is reduced to 3'-keto-deoxynucleotide concomitant with formation of a disulfide anion radical between two cysteine residues.
  • A proton-coupled electron-transfer from the disulfide radical to the substrate generates a 3'-deoxynucleotide radical, and the the final product is formed when the hydrogen atom that was initially removed from the 3'-position of the nucleotide by the thiyl radical is returned to the same position.
  • The disulfide bridge is reduced by the action of thioredoxin.
  • Cf. EC 1.1.98.6 and EC 1.17.4.2.
 24 A0A0H4L2Q0 A0A0H4L2Q0 A0A0M8K8F7 A0A0M8K8F7 A0A101DKV7 A0A101DKV7 A0A160VQW7 A0A160VQW7 A0A1A0CJU4 A0A1A0CJU4
(14 more...)
DNA topoisomerase (ATP-hydrolyzing). [EC: 5.99.1.3]
ATP-dependent breakage, passage and rejoining of double-stranded DNA.
  • Can introduce negative superhelical turns into double-stranded circular DNA.
  • One unit has nicking-closing activity, and another catalyzes super- twisting and hydrolysis of ATP (cf. EC 5.99.1.2).
 12 A0A0S4PDL9 A0A0S4PDL9 A0A1J4VQN1 A0A1J4VQN1 L0K1G7 L0K1G7 S6D1B4 S6D1B4 U2F490 U2F490
(2 more...)
H(+)-transporting two-sector ATPase. [EC: 3.6.3.14]
ATP + H(2)O + H(+)(In) = ADP + phosphate + H(+)(Out).
  • A multisubunit non-phosphorylated ATPase that is involved in the transport of ions.
  • Large enzymes of mitochondria, chloroplasts and bacteria with a membrane sector (F(o), V(o), A(o)) and a cytoplasmic-compartment sector (F(1), V(1), A(1)).
  • The F-type enzymes of the inner mitochondrial and thylakoid membranes act as ATP synthases.
  • All of the enzymes included here operate in a rotational mode, where the extramembrane sector (containing 3 alpha- and 3 beta-subunits) is connected via the delta-subunit to the membrane sector by several smaller subunits.
  • Within this complex, the gamma- and epsilon-subunits, as well as the 9-12 c subunits rotate by consecutive 120 degree angles and perform parts of ATP synthesis.
  • This movement is driven by the H(+) electrochemical potential gradient.
  • The V-type (in vacuoles and clathrin-coated vesicles) and A-type (archaeal) enzymes have a similar structure but, under physiological conditions, they pump H(+) rather than synthesize ATP.
  • Formerly EC 3.6.1.34.
 8 A0A0D5ZE85 A0A0D5ZE85 H3ZKG9 H3ZKG9 O57728 O57728 Q9UXU7 Q9UXU7
UDP-glucose 6-dehydrogenase. [EC: 1.1.1.22]
UDP-glucose + 2 NAD(+) + H(2)O = UDP-glucuronate + 2 NADH.
  • Also acts on UDP-2-deoxyglucose.
 8 A6UU28 A6UU28 C9REC8 C9REC8 F6BA94 F6BA94 F8AML2 F8AML2
DNA-directed RNA polymerase. [EC: 2.7.7.6]
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
  • Catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
  • Can initiate a chain de novo.
  • In eukaryotes three forms of the enzyme have been distinguished on the basis of sensitivity of alpha-amanitin, and the type of RNA synthesized.
  • See also EC 2.7.7.19 and EC 2.7.7.48.
 6 F6BAZ0 F6BAZ0 H1KXS2 H1KXS2 Q58446 Q58446
DNA helicase. [EC: 3.6.4.12]
ATP + H(2)O = ADP + phosphate.
  • DNA helicases utilize the energy from ATP hydrolysis to unwind double-stranded DNA.
  • Some of them unwind duplex DNA with a 3' to 5' polarity (1,3,5,8), other show 5' to 3' polarity (10,11,12,13) or unwind DNA in both directions (14,15).
  • Some helicases unwind DNA as well as RNA (4,9).
  • May be identical with EC 3.6.4.13 (RNA helicase).
 4 Q5JGV6 Q5JGV6 W0I817 W0I817
Endopeptidase La. [EC: 3.4.21.53]
Hydrolysis of proteins in presence of ATP.
  • ATP hydrolysis is linked with peptide bond hydrolysis.
  • Vanadate inhibits both reactions.
  • A similar enzyme occurs in animal mitochondria.
  • Belongs to peptidase family S16.
 2 D2RHE5 D2RHE5
Ribonucleoside-triphosphate reductase (thioredoxin). [EC: 1.17.4.2]
2'-deoxyribonucleoside triphosphate + thioredoxin disulfide + H(2)O = ribonucleoside triphosphate + thioredoxin.
  • The enzyme, characterized from the bacterium Lactobacillus leichmannii, is similar to class II ribonucleoside-diphosphate reductase (cf. EC 1.17.4.1); however, it is specific for the triphosphate versions of its substrates.
  • The enzyme contains an adenosylcobalamin cofactor that is involved in generation of a transient thiyl radical on a cysteine residue.
  • This radical attacks the substrate, forming a ribonucleotide 3'-radical, followed by water loss to form a ketyl radical.
  • The ketyl radical is reduced to 3'-keto-deoxynucleotide concomitant with formation of a disulfide anion radical between two cysteine residues.
  • A proton-coupled electron-transfer from the disulfide radical to the substrate generates a 3'-deoxynucleotide radical, and the the final product is formed when the hydrogen atom that was initially removed from the 3'-position of the nucleotide by the thiyl radical is returned to the same position.
  • The disulfide bridge is reduced by the action of thioredoxin.
  • Cf. EC 1.1.98.6.
 2 A0A098E9G8 A0A098E9G8