UniProt functional annotation for P0AES4



	UniProt functional annotation for P0AES4

UniProt code: P0AES4.

Organism: Escherichia coli (strain K12).

Taxonomy: Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia.

Function: A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to maintain chromosomes in an underwound state (PubMed:3031051, PubMed:186775, PubMed:7811004, PubMed:9148951, PubMed:12051842, PubMed:18642932, PubMed:19060136, PubMed:20356737, PubMed:22457353, PubMed:23294697, PubMed:19965760). This makes better substrates for topoisomerase IV (ParC and ParE) which is the main enzyme that unlinks newly replicated chromosomes in E.coli (PubMed:9334322). Gyrase catalyzes the interconversion of other topological isomers of dsDNA rings, including catenanes (PubMed:22457352). Relaxes negatively supercoiled DNA in an ATP-independent manner (PubMed:337300). E.coli gyrase has higher supercoiling activity than many other bacterial gyrases; at comparable concentrations E.coli gyrase introduces more supercoils faster than M.tuberculosis gyrase, while M.tuberculosis gyrase has higher decatenation than supercoiling activity compared to E.coli (PubMed:22457352). E.coli makes 15% more negative supercoils in pBR322 plasmid DNA than S.typhimurium; the S.typhimurium GyrB subunit is toxic in E.coli, while the E.coli copy can be expressed in S.typhimurium even though the 2 subunits have 777/804 residues identical (PubMed:17400739). The enzymatic differences between E.coli gyrase and topoisomerase IV are largely due to the GyrA C-terminal domain (approximately residues 524-841) and specifically the GyrA-box (PubMed:8962066, PubMed:16332690). {ECO:0000269|PubMed:12051842, ECO:0000269|PubMed:16332690, ECO:0000269|PubMed:17400739, ECO:0000269|PubMed:18642932, ECO:0000269|PubMed:186775, ECO:0000269|PubMed:19060136, ECO:0000269|PubMed:19965760, ECO:0000269|PubMed:20356737, ECO:0000269|PubMed:22457352, ECO:0000269|PubMed:22457353, ECO:0000269|PubMed:23294697, ECO:0000269|PubMed:3031051, ECO:0000269|PubMed:337300, ECO:0000269|PubMed:7811004, ECO:0000269|PubMed:8962066, ECO:0000269|PubMed:9148951, ECO:0000269|PubMed:9334322}.

Function: Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.

Catalytic activity: Reaction=ATP-dependent breakage, passage and rejoining of double- stranded DNA.; EC=5.6.2.2; Evidence={ECO:0000255|HAMAP-Rule:MF_01897, ECO:0000269|PubMed:12051842, ECO:0000269|PubMed:18642932, ECO:0000269|PubMed:186775, ECO:0000269|PubMed:19965760, ECO:0000269|PubMed:9278055};

Activity regulation: Gyrase is the target of many classes of inhibitors, including coumarins, cyclothialidines, pyrrolopyrimidines, pyrazolthiazoles and (fluoro)quinolones. Quinolones bind GyrA when the enzyme is complexed with DNA and trap the enzyme in a covalent reaction intermediate with DNA (PubMed:3031051, PubMed:12051842). Coumarins bind to GyrB and are competitive inhibitors of its ATPase activity (PubMed:7811004). Cyclothialidines also bind GyrB and are ATPase competitive inhibitors; they seem to act differently from coumarins (PubMed:7811004). Pyrrolopyrimidines inhibit both GyrB and its paralog in topoisomerase IV (parE) (PubMed:23294697). Pyrazolthiazoles also inhibit the ATPase activity of GyrB (PubMed:20356737). DNA supercoiling and relaxation are both inhibited by oxolinic acid (PubMed:337300). Acriflavine inhibits supercoiling activity and DNA-stimulated ATPase activity (PubMed:9148951). DNA supercoiling activity is protected from fluoroquinolone inhibition by QnrB4; QnrB4 has no effect on supercoiling activity alone (PubMed:19060136). {ECO:0000269|PubMed:19060136, ECO:0000269|PubMed:20356737, ECO:0000269|PubMed:23294697, ECO:0000269|PubMed:337300, ECO:0000269|PubMed:7811004, ECO:0000269|PubMed:9148951}.

Subunit: Heterotetramer, composed of two GyrA and two GyrB chains (PubMed:9148951, PubMed:12051842). In the heterotetramer, GyrA contains the active site tyrosine that forms a transient covalent intermediate with the DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis (PubMed:12051842, PubMed:18642932, PubMed:19965760, PubMed:9148951). Can form a 2:2 complex with toxin CcdB in which GyrA is inactive; rejuvenation of GyrA(2)CcdB(2) is effected by CcdA (PubMed:15854646, PubMed:1324324, PubMed:8254658, PubMed:8604132). {ECO:0000269|PubMed:12051842, ECO:0000269|PubMed:1324324, ECO:0000269|PubMed:15854646, ECO:0000269|PubMed:18642932, ECO:0000269|PubMed:19965760, ECO:0000269|PubMed:8254658, ECO:0000269|PubMed:8604132, ECO:0000269|PubMed:9148951}.

Subcellular location: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01897}.

Domain: An N-terminal fragment (residues 1-523) can be reconstituted with GyrB, but the complex no longer has negative supercoiling or ATP- independent DNA relaxation activities, although it is capable of DNA cleavage; ATP-dependent relaxation is inhibited by novobiocin and non- hydrolyzable ATP analogs (PubMed:8962066). The fragment has ATP- dependent DNA relaxation and 30-fold improved decatenation activities, unlike holoenzyme it preferentially binds supercoiled DNA (PubMed:8962066). This N-terminal fragment becomes a topoisomerase IV- like enzyme; it poorly complements a temperature-sensitive parC mutation (parC is the topoisomerase IV paralog of gyrA) (PubMed:8962066). {ECO:0000269|PubMed:8962066}.

Domain: The C-terminal domain (CTD, approximately residues 535-841) contains 6 tandemly repeated subdomains known as blades, each of which is composed of a 4-stranded antiparallel beta-sheet (PubMed:15897198). The blades form a circular-shaped beta-pinwheel fold arranged in a spiral around a screw axis, to which DNA probably binds, inducing strong positive superhelicity (about 0.8 links/protein) (PubMed:15897198). The non-conserved, C-terminal acidic tail (residues 842-875) regulates wrapping and DNA-binding by the CTD; deletions within the tail show it is autoinhibitory for DNA wrapping and binding, and couples ATP hydrolysis to DNA strand passage (PubMed:22457353). The GyrA-box is a 7 amino acid motif found in the first blade of the CTD which is discriminative for gyrase versus topoisomerase IV activity (PubMed:9426128). The GyrA-box is required for wrapping of DNA around gyrase, and thus is essential for the DNA supercoiling activity but not DNA relaxation or decatenation activities of gyrase (PubMed:16332690). {ECO:0000269|PubMed:15897198, ECO:0000269|PubMed:16332690, ECO:0000269|PubMed:22457353, ECO:0000305|PubMed:9426128}.

Miscellaneous: When the enzyme transiently cleaves DNA a phosphotyrosine bond is formed between GyrA and DNA (PubMed:3031051). In the presence of quinolones this intermediate can be trapped and is used as an indicator of drug toxicity (PubMed:12051842). The enzyme-DNA intermediate is also the target of a number of topoisomerase poisons, including toxin CcdB (PubMed:1324324, PubMed:8254658). {ECO:0000269|PubMed:1324324, ECO:0000269|PubMed:3031051, ECO:0000269|PubMed:8254658, ECO:0000305|PubMed:12051842}.

Miscellaneous: Few gyrases are as efficient as E.coli at forming negative supercoils (PubMed:22457352, PubMed:17400739). Not all organisms have 2 type II topoisomerases; in organisms with a single type II topoisomerase this enzyme also has to decatenate newly replicated chromosomes. {ECO:0000255|HAMAP-Rule:MF_01897, ECO:0000269|PubMed:17400739, ECO:0000269|PubMed:22457352}.

Similarity: Belongs to the type II topoisomerase GyrA/ParC subunit family. {ECO:0000255|HAMAP-Rule:MF_01897}.

Annotations taken from UniProtKB at the EBI.


Organism:		Escherichia coli (strain K12).
Taxonomy:		Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia.



Function:		A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to maintain chromosomes in an underwound state (PubMed:3031051, PubMed:186775, PubMed:7811004, PubMed:9148951, PubMed:12051842, PubMed:18642932, PubMed:19060136, PubMed:20356737, PubMed:22457353, PubMed:23294697, PubMed:19965760). This makes better substrates for topoisomerase IV (ParC and ParE) which is the main enzyme that unlinks newly replicated chromosomes in E.coli (PubMed:9334322). Gyrase catalyzes the interconversion of other topological isomers of dsDNA rings, including catenanes (PubMed:22457352). Relaxes negatively supercoiled DNA in an ATP-independent manner (PubMed:337300). E.coli gyrase has higher supercoiling activity than many other bacterial gyrases; at comparable concentrations E.coli gyrase introduces more supercoils faster than M.tuberculosis gyrase, while M.tuberculosis gyrase has higher decatenation than supercoiling activity compared to E.coli (PubMed:22457352). E.coli makes 15% more negative supercoils in pBR322 plasmid DNA than S.typhimurium; the S.typhimurium GyrB subunit is toxic in E.coli, while the E.coli copy can be expressed in S.typhimurium even though the 2 subunits have 777/804 residues identical (PubMed:17400739). The enzymatic differences between E.coli gyrase and topoisomerase IV are largely due to the GyrA C-terminal domain (approximately residues 524-841) and specifically the GyrA-box (PubMed:8962066, PubMed:16332690). {ECO:0000269\|PubMed:12051842, ECO:0000269\|PubMed:16332690, ECO:0000269\|PubMed:17400739, ECO:0000269\|PubMed:18642932, ECO:0000269\|PubMed:186775, ECO:0000269\|PubMed:19060136, ECO:0000269\|PubMed:19965760, ECO:0000269\|PubMed:20356737, ECO:0000269\|PubMed:22457352, ECO:0000269\|PubMed:22457353, ECO:0000269\|PubMed:23294697, ECO:0000269\|PubMed:3031051, ECO:0000269\|PubMed:337300, ECO:0000269\|PubMed:7811004, ECO:0000269\|PubMed:8962066, ECO:0000269\|PubMed:9148951, ECO:0000269\|PubMed:9334322}.



Function:		Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.


Catalytic activity:		Reaction=ATP-dependent breakage, passage and rejoining of double- stranded DNA.; EC=5.6.2.2; Evidence={ECO:0000255\|HAMAP-Rule:MF_01897, ECO:0000269\|PubMed:12051842, ECO:0000269\|PubMed:18642932, ECO:0000269\|PubMed:186775, ECO:0000269\|PubMed:19965760, ECO:0000269\|PubMed:9278055};
Activity regulation:		Gyrase is the target of many classes of inhibitors, including coumarins, cyclothialidines, pyrrolopyrimidines, pyrazolthiazoles and (fluoro)quinolones. Quinolones bind GyrA when the enzyme is complexed with DNA and trap the enzyme in a covalent reaction intermediate with DNA (PubMed:3031051, PubMed:12051842). Coumarins bind to GyrB and are competitive inhibitors of its ATPase activity (PubMed:7811004). Cyclothialidines also bind GyrB and are ATPase competitive inhibitors; they seem to act differently from coumarins (PubMed:7811004). Pyrrolopyrimidines inhibit both GyrB and its paralog in topoisomerase IV (parE) (PubMed:23294697). Pyrazolthiazoles also inhibit the ATPase activity of GyrB (PubMed:20356737). DNA supercoiling and relaxation are both inhibited by oxolinic acid (PubMed:337300). Acriflavine inhibits supercoiling activity and DNA-stimulated ATPase activity (PubMed:9148951). DNA supercoiling activity is protected from fluoroquinolone inhibition by QnrB4; QnrB4 has no effect on supercoiling activity alone (PubMed:19060136). {ECO:0000269\|PubMed:19060136, ECO:0000269\|PubMed:20356737, ECO:0000269\|PubMed:23294697, ECO:0000269\|PubMed:337300, ECO:0000269\|PubMed:7811004, ECO:0000269\|PubMed:9148951}.
Subunit:		Heterotetramer, composed of two GyrA and two GyrB chains (PubMed:9148951, PubMed:12051842). In the heterotetramer, GyrA contains the active site tyrosine that forms a transient covalent intermediate with the DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis (PubMed:12051842, PubMed:18642932, PubMed:19965760, PubMed:9148951). Can form a 2:2 complex with toxin CcdB in which GyrA is inactive; rejuvenation of GyrA(2)CcdB(2) is effected by CcdA (PubMed:15854646, PubMed:1324324, PubMed:8254658, PubMed:8604132). {ECO:0000269\|PubMed:12051842, ECO:0000269\|PubMed:1324324, ECO:0000269\|PubMed:15854646, ECO:0000269\|PubMed:18642932, ECO:0000269\|PubMed:19965760, ECO:0000269\|PubMed:8254658, ECO:0000269\|PubMed:8604132, ECO:0000269\|PubMed:9148951}.
Subcellular location:		Cytoplasm {ECO:0000255\|HAMAP-Rule:MF_01897}.
Domain:		An N-terminal fragment (residues 1-523) can be reconstituted with GyrB, but the complex no longer has negative supercoiling or ATP- independent DNA relaxation activities, although it is capable of DNA cleavage; ATP-dependent relaxation is inhibited by novobiocin and non- hydrolyzable ATP analogs (PubMed:8962066). The fragment has ATP- dependent DNA relaxation and 30-fold improved decatenation activities, unlike holoenzyme it preferentially binds supercoiled DNA (PubMed:8962066). This N-terminal fragment becomes a topoisomerase IV- like enzyme; it poorly complements a temperature-sensitive parC mutation (parC is the topoisomerase IV paralog of gyrA) (PubMed:8962066). {ECO:0000269\|PubMed:8962066}.
Domain:		The C-terminal domain (CTD, approximately residues 535-841) contains 6 tandemly repeated subdomains known as blades, each of which is composed of a 4-stranded antiparallel beta-sheet (PubMed:15897198). The blades form a circular-shaped beta-pinwheel fold arranged in a spiral around a screw axis, to which DNA probably binds, inducing strong positive superhelicity (about 0.8 links/protein) (PubMed:15897198). The non-conserved, C-terminal acidic tail (residues 842-875) regulates wrapping and DNA-binding by the CTD; deletions within the tail show it is autoinhibitory for DNA wrapping and binding, and couples ATP hydrolysis to DNA strand passage (PubMed:22457353). The GyrA-box is a 7 amino acid motif found in the first blade of the CTD which is discriminative for gyrase versus topoisomerase IV activity (PubMed:9426128). The GyrA-box is required for wrapping of DNA around gyrase, and thus is essential for the DNA supercoiling activity but not DNA relaxation or decatenation activities of gyrase (PubMed:16332690). {ECO:0000269\|PubMed:15897198, ECO:0000269\|PubMed:16332690, ECO:0000269\|PubMed:22457353, ECO:0000305\|PubMed:9426128}.
Miscellaneous:		When the enzyme transiently cleaves DNA a phosphotyrosine bond is formed between GyrA and DNA (PubMed:3031051). In the presence of quinolones this intermediate can be trapped and is used as an indicator of drug toxicity (PubMed:12051842). The enzyme-DNA intermediate is also the target of a number of topoisomerase poisons, including toxin CcdB (PubMed:1324324, PubMed:8254658). {ECO:0000269\|PubMed:1324324, ECO:0000269\|PubMed:3031051, ECO:0000269\|PubMed:8254658, ECO:0000305\|PubMed:12051842}.
Miscellaneous:		Few gyrases are as efficient as E.coli at forming negative supercoils (PubMed:22457352, PubMed:17400739). Not all organisms have 2 type II topoisomerases; in organisms with a single type II topoisomerase this enzyme also has to decatenate newly replicated chromosomes. {ECO:0000255\|HAMAP-Rule:MF_01897, ECO:0000269\|PubMed:17400739, ECO:0000269\|PubMed:22457352}.
Similarity:		Belongs to the type II topoisomerase GyrA/ParC subunit family. {ECO:0000255\|HAMAP-Rule:MF_01897}.