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PR01552

Identifier
TPISMRASE6A  [View Relations]  [View Alignment]  
Accession
PR01552
No. of Motifs
5
Creation Date
19-JUN-2001
Title
DNA topoisomerase VI subunit A (TOP6A) signature
Database References
PRINTS; PR01550 TOP6AFAMILY
PDB; 1D3Y
SCOP; 1D3Y
CATH; 1D3Y
Literature References
1. NICHOLS, M.D., DEANGELIS, K., KECK, J.L. AND BERGER, J.M.
Structure and function of an archaeal topoisomerase VI subunit with homology
to the meiotic recombination factor Spo11.
EMBO J. 18 6177-6188 (1999). 

Documentation
In all organisms, type II DNA topoisomerases are essential for untangling
chromosomal DNA [1]. The structure of the DNA-binding core of the 
Methanococcus jannaschii DNA topoisomerase VI A subunit has been determined
to 2.0A resolution [1]. The overall structure of the subunit is unique,
demonstrating that archaeal type II enzymes are distinct from other type II
topoisomerases [1]. Nevertheless, the core structure contains a pair of 
domains that are also found in type IA and classic type II topoisomerases
[1]. Such regions may form the basis of a DNA cleavage mechanism shared
among these enzymes [1]. 
 
The core A subunit is a dimer, with a deep groove spanning both protomers
[1]. The dimer architecture is such that DNA is thought to bind in the 
groove, across the A subunit interface, and the monomers are thought to
separate during DNA transport [1]. The A subunit of topoisomerase VI is 
similar to the meiotic recombination factor, Spo11.
 
TPISMRASE6A is a 5-element fingerprint that provides a signature for 
DNA topoisomerase VI subunit A. The fingerprint was derived from an initial alignment 
of 3 sequences: the motifs were drawn from short conserved regions spanning
virtually the full alignment length, focusing on those sections that
characterise the TOP6A topoisomerases but distinguish them from the closely
related SPO11 proteins. Three iterations on SPTR39_15f were required to
reach convergence, at which point a true set comprising 8 sequences was
identified. Several partial matches were also found: Q9LZ03 is a meiosis 
specific-like protein from Arabidopsis thaliana that fails to make a 
significant match with motif 2; and Q9LK56 and Q9M4A2 are DNA topoisomerase
VIA subunits from Arabidopsis thaliana that match motifs 4 and 5.
Summary Information
   8 codes involving  5 elements
1 codes involving 4 elements
0 codes involving 3 elements
2 codes involving 2 elements
Composite Feature Index
588888
410111
300000
200022
12345
True Positives
Q9HR32        Q9V134        TP6A_AERPE    TP6A_ARCFU    
TP6A_METJA TP6A_METTH TP6A_PYRHO TP6A_SULSH
True Positive Partials
Codes involving 4 elements
Q9LZ03
Codes involving 2 elements
Q9LK56 Q9M4A2
Sequence Titles
Q9HR32      DNA TOPOISOMERASE VI SUBUNIT A - Halobacterium sp. (strain NRC-1). 
Q9V134 DNA TOPOISOMERASE VI, SUBUNIT A (TOP6A) - Pyrococcus abyssi.
TP6A_AERPE TYPE II DNA TOPOISOMERASE VI SUBUNIT A (EC 5.99.1.3) - Aeropyrum pernix.
TP6A_ARCFU TYPE II DNA TOPOISOMERASE VI SUBUNIT A (EC 5.99.1.3) - Archaeoglobus fulgidus.
TP6A_METJA TYPE II DNA TOPOISOMERASE VI SUBUNIT A (EC 5.99.1.3) - Methanococcus jannaschii.
TP6A_METTH TYPE II DNA TOPOISOMERASE VI SUBUNIT A (EC 5.99.1.3) - Methanobacterium thermoautotrophicum.
TP6A_PYRHO TYPE II DNA TOPOISOMERASE VI SUBUNIT A (EC 5.99.1.3) - Pyrococcus horikoshii.
TP6A_SULSH TYPE II DNA TOPOISOMERASE VI SUBUNIT A (EC 5.99.1.3) - Sulfolobus shibatae.

Q9LZ03 MEIOSIS SPECIFIC-LIKE PROTEIN - Arabidopsis thaliana (Mouse-ear cress).

Q9LK56 DNA TOPOISOMERASE VI, SUBUNIT A - Arabidopsis thaliana (Mouse-ear cress).
Q9M4A2 PUTATIVE TOPOISOMERASE VIA - Arabidopsis thaliana (Mouse-ear cress).
Scan History
SPTR39_15f 3  100  NSINGLE    
Initial Motifs
Motif 1  width=21
Element Seqn Id St Int Rpt
PTRGLNNVYFDEESRLIRLGD TP6A_PYRHO 45 45 -
PKRTLSNTIFDPERGILVIGE TP6A_AERPE 40 40 -
PMRTLSNAIYDEKRKLLLLGE TP6A_SULSH 43 43 -

Motif 2 width=18
Element Seqn Id St Int Rpt
ENTFEDQSESDPIIEDLE TP6A_PYRHO 119 53 -
ENTWDEQKESDSVIQDIE TP6A_AERPE 121 60 -
ENTWDEQKESDSVIVDIE TP6A_SULSH 126 62 -

Motif 3 width=19
Element Seqn Id St Int Rpt
SKLGTGGWAVPGTVEHIQF TP6A_PYRHO 172 35 -
SKLGHGAYAIEPTPDLIEF TP6A_AERPE 174 35 -
SKTGHGAYAIEPTPDLIDF TP6A_SULSH 179 35 -

Motif 4 width=21
Element Seqn Id St Int Rpt
GQASRGVRRLIHRLHYEEGLP TP6A_PYRHO 228 37 -
GQPDRATRRFVRRLHEELKLP TP6A_AERPE 230 37 -
GQPDRATRRFVRRLNEELKLP TP6A_SULSH 235 37 -

Motif 5 width=24
Element Seqn Id St Int Rpt
RIEQQALANKSLEFVAKEYLPEKI TP6A_PYRHO 352 103 -
KLEIEAIASKGLKFFAYQYIPEKI TP6A_AERPE 355 104 -
KLEIEAMASKGLKFLAFQYIPEKI TP6A_SULSH 359 103 -
Final Motifs
Motif 1  width=21
Element Seqn Id St Int Rpt
PTRGLNNVYFDEEARLIKLGD Q9V134 45 45 -
PTRGLNNVYFDEESRLIRLGD TP6A_PYRHO 45 45 -
PTRSKSNIEYDEDADVWVYGD Q9HR32 38 38 -
PKRTLSNTIFDPERGILVIGE TP6A_AERPE 40 40 -
PMRTLSNAIYDEKRKLLLLGE TP6A_SULSH 43 43 -
ATRTKYNIEFNEESEVWVYGD TP6A_ARCFU 34 34 -
PSRGTSNIIYDEDKRHYVLGD TP6A_METTH 33 33 -
PIRSLSNAMFDKEKGSFTLVG TP6A_METJA 41 41 -

Motif 2 width=18
Element Seqn Id St Int Rpt
ENTFEDQSESDPIIEDLE Q9V134 119 53 -
ENTFEDQSESDPIIEDLE TP6A_PYRHO 119 53 -
EAQFNDQSESDKLVEDLE Q9HR32 110 51 -
ENTWDEQKESDSVIQDIE TP6A_AERPE 121 60 -
ENTWDEQKESDSVIVDIE TP6A_SULSH 126 62 -
AAKFEEQPESDRLVEDLE TP6A_ARCFU 104 49 -
EVDFADQQESNIVGEDLE TP6A_METTH 102 48 -
EARFDDQQASNNVIEDLE TP6A_METJA 110 48 -

Motif 3 width=19
Element Seqn Id St Int Rpt
SKLGTGGWAVPGTVEHIQF Q9V134 172 35 -
SKLGTGGWAVPGTVEHIQF TP6A_PYRHO 172 35 -
EDVGQGGYQIPNNPDTIDF Q9HR32 169 41 -
SKLGHGAYAIEPTPDLIEF TP6A_AERPE 174 35 -
SKTGHGAYAIEPTPDLIDF TP6A_SULSH 179 35 -
DDVGEGGYQIPVNVDKIEF TP6A_ARCFU 163 41 -
LRSGKSGYNISPTIDEVEF TP6A_METTH 156 36 -
TKLGTGAYNIPNDVTKLNL TP6A_METJA 168 40 -

Motif 4 width=21
Element Seqn Id St Int Rpt
GQASRGVRRLIHRLHYEEGLP Q9V134 228 37 -
GQASRGVRRLIHRLHYEEGLP TP6A_PYRHO 228 37 -
GQPARATRRLTKRLHDELDLP Q9HR32 225 37 -
GQPDRATRRFVRRLHEELKLP TP6A_AERPE 230 37 -
GQPDRATRRFVRRLNEELKLP TP6A_SULSH 235 37 -
GQPARSTRRLLRRLNTELNLP TP6A_ARCFU 219 37 -
GQAARATRRFIKRVNEELNLP TP6A_METTH 212 37 -
GVPARATRRFIKRLHEEHDLP TP6A_METJA 223 36 -

Motif 5 width=24
Element Seqn Id St Int Rpt
RIEQQALANKSLEFVAKEYLPEKI Q9V134 352 103 -
RIEQQALANKSLEFVAKEYLPEKI TP6A_PYRHO 352 103 -
KAEQQALASRGLDFVTDTYLPERL Q9HR32 337 91 -
KLEIEAIASKGLKFFAYQYIPEKI TP6A_AERPE 355 104 -
KLEIEAMASKGLKFLAFQYIPEKI TP6A_SULSH 359 103 -
KSEQQALAKYGLDYVTDVYLPERL TP6A_ARCFU 331 91 -
KAEQQSFSKYGLEYVVDTYLPEKL TP6A_METTH 324 91 -
RAEQQSLAKYGLKYVVNTYLPEKI TP6A_METJA 338 94 -