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PR01098

Identifier
TOPISMRASE4B  [View Relations]  [View Alignment]  
Accession
PR01098
No. of Motifs
15
Creation Date
07-MAR-1999  (UPDATE 07-JUN-1999)
Title
Topoisomerase IV subunit B signature
Database References
PRINTS; PR00418 TPI2FAMILY
INTERPRO; IPR000411
Literature References
1. TSAI-PFLUGFELDER, M., LIU, L.F., LIU, A.A., TEWEY, K.M., WHANG-PENG, J.,
KNUTSEN, T., HUEBNER, K., CRUCE, C.M. AND WANG, J.C.
Cloning and sequencing of cDNA encoding human DNA topoisomerase II and 
localization of the gene to chromosome region 17q21-22.
PROC.NATL.ACAD.SCI.U.S.A. 85 7177-7181 (1988).
 
2. HINDS, M., DEISSEROTH, K., MAYES, J., ALTSCHULER, E., JANSEN, R., 
LEDLEY, F.D. AND ZWELLING, L.A.
Identification of a point mutation in the topoisomerase II gene from a 
human leukemia cell line containing an amscarine-resistant form of
topoisomerase II.
CANCER RES. 51 4729-4731 (1991).
 
3. WIGLEY, D.B., DAVIES, G.J., DODSON, E.J., MAXWELL, A. AND DODSON, G.
Crystal structure of an N-terminal fragment of the DNA gyrase B protein.
NATURE 351 624-629 (1991).
 
4. PENG, H. AND MARIANS, K.J.
Escherichia coli topoisomerase IV. Purification, characterization, subunit
structure, and subunit interactions.
J.BIOL.CHEM. 268 24481-24490 (1993).

Documentation
Topoisomerases catalyse the interconversion of topological isomers of DNA
and play a key role in DNA metabolism [1]. Topoisomerase I catalyses an ATP-
independent reaction, while topoisomerase II catalyses an ATP-dependent
reaction, resulting in the formation of DNA supercoils [1-3]. The supercoil
is formed by transient cleavage in both strands of double-stranded DNA,
followed by the passage of a segment of DNA through the break, and break
ligation [3]. Eukaryotic enzymes can form both positive and negative
supercoils, while prokaryotic enzymes form only negative supercoils.
 
Eukaryotic topoisomerase II exists as a homodimer; in bacteriophage T4 it 
consists of 3 heterologous subunits; in prokaryotes it exists as a tetramer
of 2 subunits (2 each of gyrA and gyrB); and in E.coli, a second type II
topoisomerase, involved in chromosome segregation (topoisomerase IV),
consists of 2 subunits (parC and parE). GyrB, parE, and the product of 
bacteriophage T4 gene 39, are all similar to the eukaryotic proteins [1-3].
 
Investigations have shown that full-length ParC and ParE are required to
reconstitute Topo IV activity, while truncated ParC and ParE are inactive 
[4]. Topo IV activity is inhibited by quinolone and coumarin antibiotics, 
but the concentrations required for 50% inhibition of activity are 3-30-fold
higher than those required to inhibit DNA gyrase [4]. Norfloxacin-induced 
DNA cleavage patterns of Topo IV and DNA gyrase are distinct, but over-
lapping. The native forms of ParC and ParE are respectively a dimer and a
monomer, while the active form of Topo IV is a heterotetramer, ParC2ParE2. 
It is thought that the inactivity of truncated forms of ParC and ParE might
be attributed to their failure to form the heterotetramer [4]. 
 
TOPISMRASE4B is a 15-element fingerprint that provides a signature for
topoisomerase IV subunit B. The fingerprint was derived from an initial
alignment of 3 sequences: the motifs were drawn from conserved regions
spanning the full alignment length, focusing on those regions that
characterise topoisomerase IV but distinguish it from closely related
members of the topoisomerase II family. Two iterations on OWL31.1 were
required to reach convergence, at which point a true set comprising 4
sequences was identified. A single partial match was also found, a
topoisomerase IV subunit B fragment from Vibrio cholerae that matches 
motifs 9-12.
 
An update on SPTR37_9f identified a true set of 3 sequences, and 4
partial matches.
Summary Information
   3 codes involving 15 elements
0 codes involving 14 elements
0 codes involving 13 elements
0 codes involving 12 elements
0 codes involving 11 elements
0 codes involving 10 elements
0 codes involving 9 elements
0 codes involving 8 elements
0 codes involving 7 elements
0 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
1 codes involving 3 elements
2 codes involving 2 elements
Composite Feature Index
15333333333333333
14000000000000000
13000000000000000
12000000000000000
11000000000000000
10000000000000000
9000000000000000
8000000000000000
7000000000000000
6000000000000000
5000000000000000
4000000000000000
3011000000000100
2000001000110010
123456789101112131415
True Positives
PARE_ECOLI    PARE_HAEIN    PARE_SALTY    
True Positive Partials
Codes involving 3 elements
PARE_STRPN
Codes involving 2 elements
GYRB_MYCLE PARE_CAUCR
Sequence Titles
PARE_ECOLI  TOPOISOMERASE IV SUBUNIT B (EC 5.99.1.-) - ESCHERICHIA COLI. 
PARE_HAEIN TOPOISOMERASE IV SUBUNIT B (EC 5.99.1.-) - HAEMOPHILUS INFLUENZAE.
PARE_SALTY TOPOISOMERASE IV SUBUNIT B (EC 5.99.1.-) - SALMONELLA TYPHIMURIUM.

PARE_STRPN TOPOISOMERASE IV SUBUNIT B (EC 5.99.1.-) - STREPTOCOCCUS PNEUMONIAE.

GYRB_MYCLE DNA GYRASE SUBUNIT B (EC 5.99.1.3) - MYCOBACTERIUM LEPRAE.
PARE_CAUCR TOPOISOMERASE IV SUBUNIT B (EC 5.99.1.-) - CAULOBACTER CRESCENTUS.
Scan History
OWL31_1    2  75   NSINGLE    
SPTR37_9f 2 85 NSINGLE
Initial Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
YTDTTRPNHLGQEV PARE_ECOLI 26 26 -
YTDTTRPNHLGQEV ECOPARE 26 26 -
YTDTTRPNHLGQEV PARE_SALTY 26 26 -

Motif 2 width=15
Element Seqn Id St Int Rpt
QVYNIAFENGEKVQD PARE_ECOLI 135 95 -
QVYNIAFENGEKVQD ECOPARE 135 95 -
QVYNIAFENGEKVQD PARE_SALTY 135 95 -

Motif 3 width=16
Element Seqn Id St Int Rpt
DLQVVGTCGKRNTGTS PARE_SALTY 149 -1 -
DLQVVGTCGKRNTGTS PARE_ECOLI 149 -1 -
DLQVVGTCGKRNTGTS ECOPARE 149 -1 -

Motif 4 width=18
Element Seqn Id St Int Rpt
FDSPRFSVSRLTHVLKAK PARE_ECOLI 174 9 -
FDSPRFSVSRLMHVLKAK PARE_SALTY 174 9 -
FDSPRFSVSRLTHVLKAK ECOPARE 174 9 -

Motif 5 width=22
Element Seqn Id St Int Rpt
AVLCPGVEITFKDEINNTEQRW PARE_ECOLI 192 0 -
AVLCPGVEITFKDEVNNSEQRW PARE_SALTY 192 0 -
AVLCPGVEITFKDEINNTEQRW ECOPARE 192 0 -

Motif 6 width=24
Element Seqn Id St Int Rpt
FIGNFAGDTEAVDWALLWLPEGGE ECOPARE 238 24 -
FIGNFAGDTEAVDWALLWLPEGGE PARE_ECOLI 238 24 -
FIGNFNGETEAVDWALLWLPEGGE PARE_SALTY 238 24 -

Motif 7 width=17
Element Seqn Id St Int Rpt
FCEYRNILPRGVKLSAE ECOPARE 294 32 -
FCEYRNILPRGQKLSAE PARE_SALTY 294 32 -
FCEYRNILPRGVKLSAE PARE_ECOLI 294 32 -

Motif 8 width=16
Element Seqn Id St Int Rpt
DIWDRCAYVLSVKMQD PARE_ECOLI 311 0 -
DIWDRCAYVLSVKMQD ECOPARE 311 0 -
DIWDRCAYVLSVKMQD PARE_SALTY 311 0 -

Motif 9 width=24
Element Seqn Id St Int Rpt
SSRQCAAFVSGVVKDAFSLWLNQN PARE_SALTY 338 11 -
SSRQCAAFVSGVVKDAFILWLNQN ECOPARE 338 11 -
SSRQCAAFVSGVVKDAFILWLNQN PARE_ECOLI 338 11 -

Motif 10 width=26
Element Seqn Id St Int Rpt
VQAAELLAEMAISSAQRRMRAAKKVV ECOPARE 362 0 -
VQAAELLAEMAISSAQRRMRAAKKVV PARE_ECOLI 362 0 -
VQAAEQLAEMAIASAQRRLRARKKVV PARE_SALTY 362 0 -

Motif 11 width=22
Element Seqn Id St Int Rpt
WEVSSDEVLASQEVHDISVAIG PARE_ECOLI 448 60 -
WEVSSDEVLASQEVHDISVAIG ECOPARE 448 60 -
WEVSSDEVLASQEVHDISVAIG PARE_SALTY 448 60 -

Motif 12 width=13
Element Seqn Id St Int Rpt
GIDPDSDDLSQLR PARE_SALTY 469 -1 -
GIDPDSDDLSQLR ECOPARE 469 -1 -
GIDPDSDDLSQLR PARE_ECOLI 469 -1 -

Motif 13 width=17
Element Seqn Id St Int Rpt
CALFVKHFRALVKHGHV ECOPARE 503 21 -
CALFVKHFRALVKHGHV PARE_ECOLI 503 21 -
CALFVRHFRALVKNGHV PARE_SALTY 503 21 -

Motif 14 width=23
Element Seqn Id St Int Rpt
YALTEEEKEGVLEQLKRKKGKPN ECOPARE 537 17 -
YALTEEEKEGVLEQLKRKKGKPN PARE_ECOLI 537 17 -
YALTEEEKAGVLEQLKRKKGKPN PARE_SALTY 537 17 -

Motif 15 width=15
Element Seqn Id St Int Rpt
NTRRLVQLTIDDEDD ECOPARE 582 22 -
NTRRLVQLTISDEDD PARE_SALTY 582 22 -
NTRRLVQLTIDDEDD PARE_ECOLI 582 22 -
Final Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
YTDTTRPNHLGQEV PARE_ECOLI 26 26 -
YTDTTRPNHLGQEV PARE_SALTY 26 26 -
YTDTTRPNHLAQEV PARE_HAEIN 26 26 -

Motif 2 width=15
Element Seqn Id St Int Rpt
QVYNIAFENGEKVQD PARE_ECOLI 135 95 -
QVYNIAFENGEKVQD PARE_SALTY 135 95 -
EIYKIAFENGSKVEE PARE_HAEIN 135 95 -

Motif 3 width=16
Element Seqn Id St Int Rpt
DLQVVGTCGKRNTGTS PARE_ECOLI 149 -1 -
DLQVVGTCGKRNTGTS PARE_SALTY 149 -1 -
ELEIIGTCGRRTTGTI PARE_HAEIN 149 -1 -

Motif 4 width=18
Element Seqn Id St Int Rpt
FDSPRFSVSRLTHVLKAK PARE_ECOLI 174 9 -
FDSPRFSVSRLMHVLKAK PARE_SALTY 174 9 -
FDSAKFSVSRLRHLLRAK PARE_HAEIN 174 9 -

Motif 5 width=22
Element Seqn Id St Int Rpt
AVLCPGVEITFKDEINNTEQRW PARE_ECOLI 192 0 -
AVLCPGVEITFKDEVNNSEQRW PARE_SALTY 192 0 -
AVLCSGLEIKFIDKVNNTQDIW PARE_HAEIN 192 0 -

Motif 6 width=24
Element Seqn Id St Int Rpt
FIGNFAGDTEAVDWALLWLPEGGE PARE_ECOLI 238 24 -
FIGNFNGETEAVDWALLWLPEGGE PARE_SALTY 238 24 -
FVGEFKGANEAVSWALLWLPEGGE PARE_HAEIN 238 24 -

Motif 7 width=17
Element Seqn Id St Int Rpt
FCEYRNILPRGVKLSAE PARE_ECOLI 294 32 -
FCEYRNILPRGQKLSAE PARE_SALTY 294 32 -
FCEFRNLLPRGVKLTAD PARE_HAEIN 294 32 -

Motif 8 width=16
Element Seqn Id St Int Rpt
DIWDRCAYVLSVKMQD PARE_ECOLI 311 0 -
DIWDRCAYVLSVKMQD PARE_SALTY 311 0 -
DIWDRCSYILSLKMQD PARE_HAEIN 311 0 -

Motif 9 width=24
Element Seqn Id St Int Rpt
SSRQCAAFVSGVVKDAFILWLNQN PARE_ECOLI 338 11 -
SSRQCAAFVSGVVKDAFSLWLNQN PARE_SALTY 338 11 -
SSRQSAVFVSGVLKDAFSLWLNQN PARE_HAEIN 338 11 -

Motif 10 width=26
Element Seqn Id St Int Rpt
VQAAELLAEMAISSAQRRMRAAKKVV PARE_ECOLI 362 0 -
VQAAEQLAEMAIASAQRRLRARKKVV PARE_SALTY 362 0 -
VQDAEKLAEIAISSAQRRLRAAKKVV PARE_HAEIN 362 0 -

Motif 11 width=22
Element Seqn Id St Int Rpt
WEVSSDEVLASQEVHDISVAIG PARE_ECOLI 448 60 -
WEVSSDEVLASQEVHDISVAIG PARE_SALTY 448 60 -
WEVSPDQVLGSTEIHDIAVALG PARE_HAEIN 448 60 -

Motif 12 width=13
Element Seqn Id St Int Rpt
GIDPDSDDLSQLR PARE_ECOLI 469 -1 -
GIDPDSDDLSQLR PARE_SALTY 469 -1 -
GIDPDSNDLSQLR PARE_HAEIN 469 -1 -

Motif 13 width=17
Element Seqn Id St Int Rpt
CALFVKHFRALVKHGHV PARE_ECOLI 503 21 -
CALFVRHFRALVKNGHV PARE_SALTY 503 21 -
CALFLRHFPKLVQDGHV PARE_HAEIN 503 21 -

Motif 14 width=23
Element Seqn Id St Int Rpt
YALTEEEKEGVLEQLKRKKGKPN PARE_ECOLI 537 17 -
YALTEEEKAGVLEQLKRKKGKPN PARE_SALTY 537 17 -
YALDENEKEAILDRLKNKKGKPN PARE_HAEIN 537 17 -

Motif 15 width=15
Element Seqn Id St Int Rpt
NTRRLVQLTIDDEDD PARE_ECOLI 582 22 -
NTRRLVQLTISDEDD PARE_SALTY 582 22 -
NTRRLVQLTYDLGED PARE_HAEIN 582 22 -