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PR00696

Identifier
RSOLVASERUVC  [View Relations]  [View Alignment]  
Accession
PR00696
No. of Motifs
5
Creation Date
11-APR-1997  (UPDATE 07-JUN-1999)
Title
Crossover junction endodeoxyribonuclease RUVC signature
Database References

PROSITE; PS01321 RUVC
INTERPRO; IPR002176
PDB; 1HJR
SCOP; 1HJR
CATH; 1HJR
Literature References
1. IWASAKI, H., TAKAHAGI, M., SHIBA, T., NAKATA, A. AND SHINAGAWA, H.
Escherichia coli ruvC protein is an endonuclease that resolves the
Holliday structure.
EMBO J. 10(13) 4381-4389 (1991). 
 
2. ARIYOSHI,M., VASSYLYEV, D.G., IWASAKI, H., FUJISHIMA, A.,     
SHINAGAWA, H. AND MORIKAWA, K.                              
Preliminary crystallographic study of Escherichia coli ruvC protein:
an endonuclease specific for Holliday junctions.                                  
J.MOL.BIOL. 241 281-282 (1994). 

Documentation
The Escherichia coli ruvC gene is involved in DNA repair and in the late
step of RecE and RecF pathway recombination [1]. RuvC protein cleaves
cruciform junctions, which are formed by the extrusion of inverted repeat
sequences from a super-coiled plasmid and which are structurally analogous
to Holliday junctions, by introducing nicks into strands with the same
polarity. The nicked ends are ligated by E.coli or T4 DNA ligases. Analysis
of the cleavage sites suggests that DNA topology rather than a particular
sequence determines the cleavage site. RuvC protein also cleaves Holliday
junctions that are formed between gapped circular and linear duplex DNA by
the function of RecA protein. The active form of RuvC protein is a dimer. 
This is mechanistically suited for an endonuclease involved in swapping DNA
strands at the crossover junctions. It is inferred that RuvC protein is an
endonuclease that resolves Holliday structures in vivo [1]. 
 
The structure of E.coli ruvC is a 3-layer alpha-beta sandwich containing
a 5-stranded beta-sheet sandwiched between 5 alpha-helices [2].
 
RSOLVASERUVC is a 5-element fingerprint that provides a signature for 
crossover junction endodeoxyribonuclease ruvC. The fingerprint was derived
from an initial alignment of 5 sequences: the motifs were drawn from
conserved regions spanning the full alignment length - motif 1 spans the
first 2 strands; motif 2 encompasses strand 4 and the following loop; 
motif 3 includes part of helix 2; motif 4 spans helices 3 and 4; and 
motif 5 encompasses helix 5. A single iteration on OWL29.2 was required
to reach convergence, no further sequences being identified beyond the
starting set. A single partial match was found, SYCSLLLH82, a Synechocystis
homologue that matches motifs 1 and 4.
 
An update on SPTR37_9f identified a true set of 7 sequences, and 3
partial matches.
Summary Information
   7 codes involving  5 elements
1 codes involving 4 elements
1 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
577777
410111
310011
210010
12345
True Positives
RUVC_ANASP    RUVC_ECOLI    RUVC_HAEIN    RUVC_MYCLE    
RUVC_MYCTU RUVC_PSEAE RUVC_TREPA
True Positive Partials
Codes involving 4 elements
O84510
Codes involving 3 elements
RUVC_HELPY
Codes involving 2 elements
Q55506
Sequence Titles
RUVC_ANASP  CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUVC (EC 3.1.22.4) (HOLLIDAY JUNCTION NUCLEASE RUVC) (HOLLIDAY JUCTION RESOLVASE RUVC) - ANABAENA SP. (STRAIN PCC 7120). 
RUVC_ECOLI CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUVC (EC 3.1.22.4) (HOLLIDAY JUNCTION NUCLEASE RUVC) (HOLLIDAY JUCTION RESOLVASE RUVC) - ESCHERICHIA COLI.
RUVC_HAEIN CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUVC (EC 3.1.22.4) (HOLLIDAY JUNCTION NUCLEASE RUVC) (HOLLIDAY JUCTION RESOLVASE RUVC) - HAEMOPHILUS INFLUENZAE.
RUVC_MYCLE CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUVC (EC 3.1.22.4) (HOLLIDAY JUNCTION NUCLEASE RUVC) (HOLLIDAY JUCTION RESOLVASE RUVC) - MYCOBACTERIUM LEPRAE.
RUVC_MYCTU CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUVC (EC 3.1.22.4) (HOLLIDAY JUNCTION NUCLEASE RUVC) (HOLLIDAY JUCTION RESOLVASE RUVC) - MYCOBACTERIUM TUBERCULOSIS.
RUVC_PSEAE CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUVC (EC 3.1.22.4) (HOLLIDAY JUNCTION NUCLEASE RUVC) (HOLLIDAY JUCTION RESOLVASE RUVC) - PSEUDOMONAS AERUGINOSA.
RUVC_TREPA CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUVC (EC 3.1.22.4) (HOLLIDAY JUNCTION NUCLEASE RUVC) (HOLLIDAY JUCTION RESOLVASE RUVC) - TREPONEMA PALLIDUM.

O84510 CROSSOVER JUNCTION ENDONUCLEASE - CHLAMYDIA TRACHOMATIS.

RUVC_HELPY CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUVC (EC 3.1.22.4) (HOLLIDAY JUNCTION NUCLEASE RUVC) (HOLLIDAY JUCTION RESOLVASE RUVC) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).

Q55506 HYPOTHETICAL 18.2 KD PROTEIN - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
Scan History
OWL29_2    1  50   NSINGLE    
SPTR37_9f 2 16 NSINGLE
Initial Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
MGVDPGLTRCGLSL MTCY2276 4 4 -
LGIDPGSRITGFGV PSEASPS2 5 5 -
LGIDPGSRVTGYGV RUVC_ECOLI 4 4 -
LGIDPGSRVTGYGV RUVC_HAEIN 5 5 -
MGVDPGLTRCGLSV RUVC_MYCLE 4 4 -

Motif 2 width=17
Element Seqn Id St Int Rpt
PDYFAIEQVFMAKNADS RUVC_ECOLI 60 42 -
PTALSIEQVFMARNADS PSEASPS2 61 42 -
PEVVAIERVFSQLNVTT MTCY2276 62 44 -
PDVMAIERVFSQQNVST RUVC_MYCLE 62 44 -
PNMFAIEQVFMAKNADS RUVC_HAEIN 61 42 -

Motif 3 width=17
Element Seqn Id St Int Rpt
QAGGVIALAAAKRGVDV MTCY2276 84 5 -
QARGVAIVAAVNQELPV RUVC_ECOLI 82 5 -
QARGTAIVAAVNNDLPV RUVC_HAEIN 83 5 -
QAGGVIALAAARRGIDV RUVC_MYCLE 84 5 -
QARGAAIVAAMEEGLSV PSEASPS2 83 5 -

Motif 4 width=20
Element Seqn Id St Int Rpt
VKQTVVGIGSADKVQVQEMV RUVC_HAEIN 107 7 -
VKAAVTGNGAANKAQVTAMV RUVC_MYCLE 108 7 -
VKQAVVGTGGADKQQVQMMV PSEASPS2 107 7 -
VKAAVTGNGSADKAQVTAMV MTCY2276 108 7 -
VKQTVVGIGSAEKSQVQHMV RUVC_ECOLI 106 7 -

Motif 5 width=13
Element Seqn Id St Int Rpt
IDASDALAIALCH PSEASPS2 138 11 -
ADAADALAIAITH RUVC_HAEIN 138 11 -
ADAADALALAICH RUVC_MYCLE 140 12 -
ADAADALAIAITH RUVC_ECOLI 137 11 -
ADAADALALAICH MTCY2276 140 12 -
Final Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
LGIDPGSRVTGYGV RUVC_ECOLI 4 4 -
LGIDPGSRVTGYGV RUVC_HAEIN 5 5 -
MGVDPGLTRCGLSV RUVC_MYCLE 4 4 -
LGIDPGSRITGFGV RUVC_PSEAE 5 5 -
MGVDPGLTRCGLSL RUVC_MYCTU 4 4 -
VGIDPGLESTGYGV RUVC_TREPA 20 20 -
LGLDPGLAILGFGA RUVC_ANASP 6 6 -

Motif 2 width=17
Element Seqn Id St Int Rpt
PDYFAIEQVFMAKNADS RUVC_ECOLI 60 42 -
PNMFAIEQVFMAKNADS RUVC_HAEIN 61 42 -
PDVMAIERVFSQQNVST RUVC_MYCLE 62 44 -
PTALSIEQVFMARNADS RUVC_PSEAE 61 42 -
PEVVAIERVFSQLNVTT RUVC_MYCTU 62 44 -
PQYCAVETIYFAKNVTS RUVC_TREPA 77 43 -
PDVVAIEKLFFYRMSST RUVC_ANASP 70 50 -

Motif 3 width=17
Element Seqn Id St Int Rpt
QARGVAIVAAVNQELPV RUVC_ECOLI 82 5 -
QARGTAIVAAVNNDLPV RUVC_HAEIN 83 5 -
QAGGVIALAAARRGIDV RUVC_MYCLE 84 5 -
QARGAAIVAAMEEGLSV RUVC_PSEAE 83 5 -
QAGGVIALAAAKRGVDV RUVC_MYCTU 84 5 -
QARGVVLLAMAQQHISV RUVC_TREPA 99 5 -
QARGVVMLALAQHHLPY RUVC_ANASP 91 4 -

Motif 4 width=20
Element Seqn Id St Int Rpt
VKQTVVGIGSAEKSQVQHMV RUVC_ECOLI 106 7 -
VKQTVVGIGSADKVQVQEMV RUVC_HAEIN 107 7 -
VKAAVTGNGAANKAQVTAMV RUVC_MYCLE 108 7 -
VKQAVVGTGGADKQQVQMMV RUVC_PSEAE 107 7 -
VKAAVTGNGSADKAQVTAMV RUVC_MYCTU 108 7 -
IKKAITGIAQAEKRQVQHLV RUVC_TREPA 123 7 -
IKLALTGYGNADKSEVQEAV RUVC_ANASP 115 7 -

Motif 5 width=13
Element Seqn Id St Int Rpt
ADAADALAIAITH RUVC_ECOLI 137 11 -
ADAADALAIAITH RUVC_HAEIN 138 11 -
ADAADALALAICH RUVC_MYCLE 140 12 -
IDASDALAIALCH RUVC_PSEAE 138 11 -
ADAADALALAICH RUVC_MYCTU 140 12 -
DHAADALAVAVTH RUVC_TREPA 155 12 -
DDAADALAVALTA RUVC_ANASP 147 12 -