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PR00867

Identifier
DNAPOLG  [View Relations]  [View Alignment]  
Accession
PR00867
No. of Motifs
9
Creation Date
29-JUN-1998  (UPDATE 07-JUN-1999)
Title
DNA-polymerase gamma (family A) signature
Database References

PROSITE; PS00447 DNA_POLYMERASE_A
BLOCKS; BL00447
INTERPRO; IPR002297
PDB; 1KFS; 1KRP
SCOP; 1KFS; 1KRP
CATH; 1KFS; 1KRP
Literature References
1. JUNG, G., LEAVITT, M.C.,	HSIEH, J-C. AND	ITO, J.
Bacteriophage PRD1 DNA polymerase: Evolution of DNA	polymerases.
PROC.NATL.ACAD.SCI.U.S.A. 84 8287-8291	(1987).
 
2. DELARUE,	M., POCH, O., TORDO, N., MORAS,	D. AND ARGOS, P.
An attempt to unify	the structure of polymerases.
PROTEIN ENG. 3(6) 461-467 (1990).
 
3. GENGA, A., BIANCHI, L. AND FOURY, F.
The nuclear gene MIP1 is strictly required for mitochondrial DNA 
replication and mitochondrial DNA polymerase activity.
J.BIOL.CHEM. 261 9328-9332 (1986). 

Documentation
DNA	carries the biological information that instructs cells how to exist
in an ordered fashion: accurate replication is thus one of the most
important events in the cell life cycle. This function is mediated by
DNA-directed DNA-polymerases, which add nucleotide triphosphate (dNTP)
residues to the 5'-end of the growing DNA chain, using a complementary 
DNA as template. Small RNA molecules are generally used as primers for
chain elongation, although terminal proteins may also be used.
 
DNA-dependent DNA-polymerases have been grouped into families, denoted A, B
and X, on the basis of sequence similarities [1,2].	Members of family A, 
which includes bacterial and bacteriophage polymerases, share significant
similarity to E.coli polymerase I; hence family A is also known as the pol I
family. The	bacterial polymerases also contain an exonuclease activity,
which is coded for in the N-terminal portion. The yeast gamma polymerases
show some similarity to the prokaryotic nuclear polymerases of family A,
but their function is restricted to mitochondrial DNA replication and 
repair [3].
 
Three motifs, A, B and C, as defined by Delarue et al. [2], are seen to be 
conserved across all DNA-polymerases, with motifs A and C also seen in RNA- 
polymerases. They are centered on invariant residues, and their structural 
significance was implied from the Klenlow (E.coli) structure: motif A 
contains a strictly-conserved aspartate at the junction of a beta-strand 
and an alpha-helix; motif B contains an alpha-helix with positive charges; 
and motif C has a doublet of negative charges, located in a beta-turn-beta 
secondary structure [2]. 
 
DNAPOLG is a 9-element fingerprint that provides a signature for the DNA-
polymerase gamma family. The fingerprint was derived from an initial
alignment of 7 sequences: the motifs were drawn from conserved sections
spanning the full alignment length, focusing on those regions that
characterise the gamma polymerases but distinguish them from the rest of
the pol I family - motif 5 includes part of the region encoded by PROSITE
pattern DNA_POLYMERASE_A (PS00447), which corresponds to "motif B". Two 
iterations on OWL30.1 were required to reach convergence, at which point a
true set comprising 10 sequences was identified. A single partial match was
also found, DPOG_CHICK, a chicken gamma polymerase fragment that matches 
motifs 4-9.
 
An update on SPTR37_9f identified a true set of 7 sequences.
Summary Information
7 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
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
9777777777
8000000000
7000000000
6000000000
5000000000
4000000000
3000000000
2000000000
123456789
True Positives
DPOG_DROME    DPOG_HUMAN    DPOG_MOUSE    DPOG_PICPA    
DPOG_SCHPO DPOG_XENLA DPOG_YEAST
Sequence Titles
DPOG_DROME  DNA POLYMERASE GAMMA PRECURSOR (EC 2.7.7.7) (MITOCHONDRIAL DNA POLYMERASE CATALYTIC SUBUNIT) - DROSOPHILA MELANOGASTER (FRUIT FLY). 
DPOG_HUMAN DNA POLYMERASE GAMMA (EC 2.7.7.7) (MITOCHONDRIAL DNA POLYMERASE CATALYTIC SUBUNIT) - HOMO SAPIENS (HUMAN).
DPOG_MOUSE DNA POLYMERASE GAMMA (EC 2.7.7.7) (MITOCHONDRIAL DNA POLYMERASE CATALYTIC SUBUNIT) - MUS MUSCULUS (MOUSE).
DPOG_PICPA DNA POLYMERASE GAMMA (EC 2.7.7.7) (MITOCHONDRIAL DNA POLYMERASE CATALYTIC SUBUNIT) - PICHIA PASTORIS (YEAST).
DPOG_SCHPO DNA POLYMERASE GAMMA (EC 2.7.7.7) (MITOCHONDRIAL DNA POLYMERASE CATALYTIC SUBUNIT) - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
DPOG_XENLA DNA POLYMERASE GAMMA (EC 2.7.7.7) (MITOCHONDRIAL DNA POLYMERASE CATALYTIC SUBUNIT) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
DPOG_YEAST DNA POLYMERASE GAMMA (EC 2.7.7.7) (MITOCHONDRIAL DNA POLYMERASE CATALYTIC SUBUNIT) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
Scan History
OWL30_1    2  100  NSINGLE    
SPTR37_9f 2 10 NSINGLE
Initial Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
LPPLYGDNLDQHF DPOG_HUMAN 127 127 -
LPRLFGGNLDQHF DPOG_MOUSE 110 110 -
LPKMYGNNIEEHF DPOG_XENLA 101 101 -
LPSLQGNTLDEHF DPOG_PICPA 75 75 -
LPPLQGKTISEHF DPOG_SCHPO 100 100 -
LPPLQGRSLDEHF DPOG_YEAST 101 101 -
LPALRGANIEEHF DPOG_DROME 112 112 -

Motif 2 width=15
Element Seqn Id St Int Rpt
GHNVSFDRAHIREQY DPOG_HUMAN 268 128 -
GHNVSFDRAHIREQY DPOG_MOUSE 251 128 -
GHNVSFDRAHIKEQY DPOG_XENLA 242 128 -
GHNVSYDRARALEEY DPOG_PICPA 200 112 -
GHNVSFDRQRIREEY DPOG_SCHPO 223 110 -
GHNVAYDRARVLEEY DPOG_YEAST 224 110 -
GHNVSYDRARLKEQY DPOG_DROME 257 132 -

Motif 3 width=10
Element Seqn Id St Int Rpt
PLFLERCPHP DPOG_HUMAN 412 129 -
PLFLERCPHP DPOG_MOUSE 394 128 -
PLFMERCPHP DPOG_XENLA 386 129 -
PKFKKLIPHP DPOG_PICPA 353 138 -
PQFLEVCPHP DPOG_SCHPO 368 130 -
PVFLKKCPHP DPOG_YEAST 360 121 -
PLYAERFPHP DPOG_DROME 379 107 -

Motif 4 width=27
Element Seqn Id St Int Rpt
GTITRRAVEPTWLTASNARPDRVGSEL DPOG_HUMAN 848 426 -
GTITRRAVEPTWLTASNARPDRVGSEL DPOG_MOUSE 826 422 -
GTITRRAVEPTWLTASNARADRVGSEL DPOG_XENLA 818 422 -
GTITRRAVENTWLTASNAKKNRLGSEL DPOG_PICPA 621 258 -
GTVTRRAVENTWLTASNSKKNRLGSEL DPOG_SCHPO 639 261 -
GTITRRAVENAWLTASNAKANRIGSEL DPOG_YEAST 651 281 -
GTLTRRAMEPTWMTASNSRPDRLGSEL DPOG_DROME 766 377 -

Motif 5 width=9
Element Seqn Id St Int Rpt
NYGRIYGAG DPOG_HUMAN 950 75 -
NYGRIYGAG DPOG_MOUSE 928 75 -
NYGRIYGAG DPOG_XENLA 920 75 -
NYGRIYGAG DPOG_PICPA 722 74 -
NYGRLYGAG DPOG_SCHPO 740 74 -
NYGRIYGAG DPOG_YEAST 752 74 -
NYARIYGAG DPOG_DROME 868 75 -

Motif 6 width=14
Element Seqn Id St Int Rpt
WKGGTESEMFNKLE DPOG_HUMAN 1049 90 -
WTGGTESEMFNKLE DPOG_MOUSE 1027 90 -
WTGGTESQMFNKLE DPOG_XENLA 1018 89 -
WYGGSESIIFNRLE DPOG_PICPA 774 43 -
WSQGTESFVFNKLE DPOG_SCHPO 801 52 -
WYGGSESILFNKLE DPOG_YEAST 805 44 -
WQGGTESAMFNRLE DPOG_DROME 953 76 -

Motif 7 width=17
Element Seqn Id St Int Rpt
SRVNWVVQSSAVDYLHL DPOG_HUMAN 1095 32 -
SRVNWVVQSSAVDYLHL DPOG_MOUSE 1073 32 -
SRVNWVVQSSAVDYLHL DPOG_XENLA 1064 32 -
SRINWAIQSSGVDYLHL DPOG_PICPA 821 33 -
SRVNWAIQSSAVDYLHL DPOG_SCHPO 848 33 -
SRINWAIQSSGVDYLHL DPOG_YEAST 852 33 -
TRINWVVQSGAVDFLHL DPOG_DROME 1002 35 -

Motif 8 width=16
Element Seqn Id St Int Rpt
RAALALQITNLLTRCM DPOG_HUMAN 1148 36 -
RAALALQITNLLTRCM DPOG_MOUSE 1126 36 -
RAALALQITNLLTRCM DPOG_XENLA 1117 36 -
RAAYALQISNLWTRAM DPOG_PICPA 874 36 -
RVAFALQVANLWTRAF DPOG_SCHPO 901 36 -
RAAMALQISNIWTRAM DPOG_YEAST 905 36 -
KAALAMHITNLMTRSF DPOG_DROME 1052 33 -

Motif 9 width=17
Element Seqn Id St Int Rpt
FAYKLGLNDLPQSVAFF DPOG_HUMAN 1164 0 -
FAYKLGLNDLPQSVAFF DPOG_MOUSE 1142 0 -
FASRLGIQDVPQSVAFF DPOG_XENLA 1133 0 -
FCQQLGINEVPQSCAFF DPOG_PICPA 890 0 -
FCQRLGINELPQSVAFF DPOG_SCHPO 917 0 -
FCQQMGINELPQNCAFF DPOG_YEAST 921 0 -
CVSRIGLQDLPMSVAFF DPOG_DROME 1068 0 -
Final Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
LPPLYGDNLDQHF DPOG_HUMAN 127 127 -
LPRLFGGNLDQHF DPOG_MOUSE 110 110 -
LPKMYGNNIEEHF DPOG_XENLA 101 101 -
LPSLQGNTLDEHF DPOG_PICPA 75 75 -
LPPLQGKTISEHF DPOG_SCHPO 100 100 -
LPPLQGRSLDEHF DPOG_YEAST 101 101 -
LPALRGANIEEHF DPOG_DROME 112 112 -

Motif 2 width=15
Element Seqn Id St Int Rpt
GHNVSFDRAHIREQY DPOG_HUMAN 268 128 -
GHNVSFDRAHIREQY DPOG_MOUSE 251 128 -
GHNVSFDRAHIKEQY DPOG_XENLA 242 128 -
GHNVSYDRARALEEY DPOG_PICPA 200 112 -
GHNVSFDRQRIREEY DPOG_SCHPO 223 110 -
GHNVAYDRARVLEEY DPOG_YEAST 224 110 -
GHNVSYDRARLKEQY DPOG_DROME 257 132 -

Motif 3 width=10
Element Seqn Id St Int Rpt
PLFLERCPHP DPOG_HUMAN 412 129 -
PLFLERCPHP DPOG_MOUSE 394 128 -
PLFMERCPHP DPOG_XENLA 386 129 -
PKFKKLIPHP DPOG_PICPA 353 138 -
PQFLEVCPHP DPOG_SCHPO 368 130 -
PVFLKKCPHP DPOG_YEAST 360 121 -
PLYAERFPHP DPOG_DROME 379 107 -

Motif 4 width=27
Element Seqn Id St Int Rpt
GTITRRAVEPTWLTASNARPDRVGSEL DPOG_HUMAN 848 426 -
GTITRRAVEPTWLTASNARPDRVGSEL DPOG_MOUSE 826 422 -
GTITRRAVEPTWLTASNARADRVGSEL DPOG_XENLA 818 422 -
GTITRRAVENTWLTASNAKKNRLGSEL DPOG_PICPA 621 258 -
GTVTRRAVENTWLTASNSKKNRLGSEL DPOG_SCHPO 639 261 -
GTITRRAVENAWLTASNAKANRIGSEL DPOG_YEAST 651 281 -
GTLTRRAMEPTWMTASNSRPDRLGSEL DPOG_DROME 766 377 -

Motif 5 width=9
Element Seqn Id St Int Rpt
NYGRIYGAG DPOG_HUMAN 950 75 -
NYGRIYGAG DPOG_MOUSE 928 75 -
NYGRIYGAG DPOG_XENLA 920 75 -
NYGRIYGAG DPOG_PICPA 722 74 -
NYGRLYGAG DPOG_SCHPO 740 74 -
NYGRIYGAG DPOG_YEAST 752 74 -
NYARIYGAG DPOG_DROME 868 75 -

Motif 6 width=14
Element Seqn Id St Int Rpt
WKGGTESEMFNKLE DPOG_HUMAN 1049 90 -
WTGGTESEMFNKLE DPOG_MOUSE 1027 90 -
WTGGTESQMFNKLE DPOG_XENLA 1018 89 -
WYGGSESIIFNRLE DPOG_PICPA 774 43 -
WSQGTESFVFNKLE DPOG_SCHPO 801 52 -
WYGGSESILFNKLE DPOG_YEAST 805 44 -
WQGGTESAMFNRLE DPOG_DROME 953 76 -

Motif 7 width=17
Element Seqn Id St Int Rpt
SRVNWVVQSSAVDYLHL DPOG_HUMAN 1095 32 -
SRVNWVVQSSAVDYLHL DPOG_MOUSE 1073 32 -
SRVNWVVQSSAVDYLHL DPOG_XENLA 1064 32 -
SRINWAIQSSGVDYLHL DPOG_PICPA 821 33 -
SRVNWAIQSSAVDYLHL DPOG_SCHPO 848 33 -
SRINWAIQSSGVDYLHL DPOG_YEAST 852 33 -
TRINWVVQSGAVDFLHL DPOG_DROME 1002 35 -

Motif 8 width=16
Element Seqn Id St Int Rpt
RAALALQITNLLTRCM DPOG_HUMAN 1148 36 -
RAALALQITNLLTRCM DPOG_MOUSE 1126 36 -
RAALALQITNLLTRCM DPOG_XENLA 1117 36 -
RAAYALQISNLWTRAM DPOG_PICPA 874 36 -
RVAFALQVANLWTRAF DPOG_SCHPO 901 36 -
RAAMALQISNIWTRAM DPOG_YEAST 905 36 -
KAALAMHITNLMTRSF DPOG_DROME 1052 33 -

Motif 9 width=17
Element Seqn Id St Int Rpt
FAYKLGLNDLPQSVAFF DPOG_HUMAN 1164 0 -
FAYKLGLNDLPQSVAFF DPOG_MOUSE 1142 0 -
FASRLGIQDVPQSVAFF DPOG_XENLA 1133 0 -
FCQQLGINEVPQSCAFF DPOG_PICPA 890 0 -
FCQRLGINELPQSVAFF DPOG_SCHPO 917 0 -
FCQQMGINELPQNCAFF DPOG_YEAST 921 0 -
CVSRIGLQDLPMSVAFF DPOG_DROME 1068 0 -