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PR00870

Identifier
DNAPOLXBETA  [View Relations]  [View Alignment]  
Accession
PR00870
No. of Motifs
6
Creation Date
29-JUN-1998  (UPDATE 14-JUN-1999)
Title
DNA-polymerase family X pol beta-like signature
Database References
PRINTS; PR90005 DNADNAPOL; PR00869 DNAPOLX
INTERPRO; IPR002008
PDB; 1BPY; 1BPX
SCOP; 1BPY; 1BPX
CATH; 1BPY; 1BPX
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)

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 X
encompass two distinct polymerase enzymes that have similar functionality:
vertebrate polymerase beta (yeast pol 4), and terminal deoxynucleotidyl-
transferase (TdT) (EC 2.7.7.31). The former functions in DNA repair, while
the latter terminally adds single nucleotides to polydeoxynucleotide chains.
Both enzymes catalyse addition of nucleotides in a distributive manner, 
i.e. they dissociate after the addition of a single nucleotide.
 
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]. 
 
DNAPOLXBETA is a 6-element fingerprint that provides a signature for the
DNA-polymerase X pol beta-like 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 beta-like proteins but distinguish them from the TdT and X
families - motif 1 spans helix 4; motif 2 straddles helix 10 and strand 1; 
motif 3, which corresponds to "motif C", spans strands 3 and 4, and helix 12,
and includes two of the active site Asps; motif 4, which corresponds to 
"motif A", encodes strand 7, which also contains an active site Asp; motif 5
spans the terminal section of helix 15; and motif 6 encodes helices 17 and 
18. Two iterations on OWL30.1 were required to reach convergence, at which
point a true set comprising 7 sequences was identified. Several partial
matches were also found: two of these, G69172 and YA26_SCHPO, are divergent
family members, and the remainder are members of the TdT family.
 
An update on SPTR37_9f identified a true set of 5 sequences, and 12
partial matches.
Summary Information
   5 codes involving  6 elements
0 codes involving 5 elements
1 codes involving 4 elements
0 codes involving 3 elements
10 codes involving 2 elements
Composite Feature Index
6555555
5000000
4101011
3000000
2219107
123456
True Positives
DPO4_YEAST    DPOB_HUMAN    DPOB_RAT      DPOB_XENLA    
Q23687
True Positive Partials
Codes involving 4 elements
O26650
Codes involving 2 elements
CLPC_ODOSI O67416 P77987 TDT_BOVIN
TDT_CHICK TDT_HUMAN TDT_MOUSE TDT_ONCMY
TDT_XENLA YA26_SCHPO
Sequence Titles
DPO4_YEAST  DNA POLYMERASE IV (EC 2.7.7.7) (POL IV) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). 
DPOB_HUMAN DNA POLYMERASE BETA (EC 2.7.7.7) - HOMO SAPIENS (HUMAN).
DPOB_RAT DNA POLYMERASE BETA (EC 2.7.7.7) - RATTUS NORVEGICUS (RAT).
DPOB_XENLA DNA POLYMERASE BETA (EC 2.7.7.7) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
Q23687 DNA POLYMERASE BETA - CRITHIDIA FASCICULATA.

O26650 DNA-DEPENDENT DNA POLYMERASE FAMILY X - METHANOBACTERIUM THERMOAUTOTROPHICUM.

CLPC_ODOSI ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA HOMOLOG - ODONTELLA SINENSIS.
O67416 DNA POLYMERASE BETA FAMILY - AQUIFEX AEOLICUS.
P77987 DNA POLYMERASE FAMILY X (EC 2.7.7.7) (DNA-DIRECTED DNA POLYMERASE) (DNA NUCLEOTIDYLTRANSFERASE (DNA-DIRECTED)) - THERMUS AQUATICUS (SUBSP. THERMOPHILUS).
TDT_BOVIN DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITION ENZYME) (TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE) (TDT) (TERMINAL TRANSFERASE) - BOS TAURUS (BOVINE).
TDT_CHICK DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITION ENZYME) (TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE) (TERMINAL TRANSFERASE) - GALLUS GALLUS (CHICKEN).
TDT_HUMAN DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITION ENZYME) (TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE) (TERMINAL TRANSFERASE) - HOMO SAPIENS (HUMAN).
TDT_MOUSE DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITION ENZYME) (TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE) (TDT) (TERMINAL TRANSFERASE) - MUS MUSCULUS (MOUSE).
TDT_ONCMY DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITION ENZYME) (TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE) (TERMINAL TRANSFERASE) - ONCORHYNCHUS MYKISS (RAINBOW TROUT) (SALMO GAIRDNERI).
TDT_XENLA DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITION ENZYME) (TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE) (TDT) (TERMINAL TRANSFERASE) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
YA26_SCHPO HYPOTHETICAL DNA POLYMERASE BETA-LIKE PROTEIN C2F7.06C - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
Scan History
OWL30_1    2  500  NSINGLE    
SPTR37_9f 2 100 NSINGLE
Initial Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
GVGTKIAEKIDEFLATGK DPOB_HUMAN 63 63 -
GVGAKIAEKIDEFLATGK XLY15732 64 64 -
GFGAKLLKKAEEIMATGK A55874 64 64 -
GVGTKIAEKIDEFLATGK RATPOLB1 64 64 -
GVGTKIAEKIDEFLATGK HUMPOLB 64 64 -
NIGPSIAKKIQVILDTGV DPO4_YEAST 239 239 -
GVGTKIAEKIDEFLATGK DPOB_RAT 63 63 -

Motif 2 width=15
Element Seqn Id St Int Rpt
RIGLKYFEDFEKRIP DPOB_RAT 136 55 -
LFGWSYYDDWLCKMS DPO4_YEAST 313 56 -
RIGLKYFGDFEKRIP HUMPOLB 137 55 -
RIGLKYFEDFEKRIP RATPOLB1 137 55 -
RVGIKYFYDINEKIP A55874 140 58 -
KIGLKHFDDFEKRIP XLY15732 137 55 -
RIGLKYFGDFEKRIP DPOB_HUMAN 136 55 -

Motif 3 width=20
Element Seqn Id St Int Rpt
VCGSFRRGAESSGDMDVLLT RATPOLB1 177 25 -
VCGSFRRGAESSGDMDVLLT HUMPOLB 177 25 -
LQGSYNRGYSKCGDIDLLFF DPO4_YEAST 353 25 -
VCGSFRRGAESSGDMDVLLT DPOB_RAT 176 25 -
VCGSFRRGAESSGDMDVLLT DPOB_HUMAN 176 25 -
ISGTYRRRHPFSGDVDALLS A55874 181 26 -
VCGSFRRGAESSGDMDILLT XLY15732 177 25 -

Motif 4 width=9
Element Seqn Id St Int Rpt
RRIDIRLYP HUMPOLB 253 56 -
RRVDIRLIE A55874 268 67 -
RRIDIRLIP DPOB_HUMAN 252 56 -
RRLDFFCCK DPO4_YEAST 498 125 -
RRIDIRLIP DPOB_RAT 252 56 -
RRIDIRLIP XLY15732 252 55 -
RRIDIRLIP RATPOLB1 253 56 -

Motif 5 width=8
Element Seqn Id St Int Rpt
GVLYFTGS DPOB_HUMAN 267 6 -
GVLYFTGS XLY15732 267 6 -
GVLYFTGS HUMPOLB 268 6 -
GVLYFTGS RATPOLB1 268 6 -
AMLTFTGS A55874 283 6 -
GVLYFTGS DPOB_RAT 267 6 -
GRIHYTGS DPO4_YEAST 513 6 -

Motif 6 width=18
Element Seqn Id St Int Rpt
EKDIFDYIQWKYREPKDR HUMPOLB 316 40 -
EKDIFDYIQWKYREPKDR XLY15732 315 40 -
EQDIFDYIQWRYREPKDR DPOB_RAT 315 40 -
ERRIFELLNLKYAEPEHR DPO4_YEAST 555 34 -
EKDIFDYIQWKYREPKDR DPOB_HUMAN 315 40 -
EQDVFDALGMPYAKPENR A55874 357 66 -
EQDIFDYIQWRYREPKDR RATPOLB1 316 40 -
Final Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
GVGTKIAEKIDEFLATGK DPOB_HUMAN 63 63 -
GVGTKIAEKIDEFLATGK DPOB_RAT 63 63 -
GVGAKIAEKIDEFLATGK DPOB_XENLA 63 63 -
GFGAKLLKKAEEIMATGK Q23687 64 64 -
NIGPSIAKKIQVILDTGV DPO4_YEAST 239 239 -

Motif 2 width=15
Element Seqn Id St Int Rpt
RIGLKYFGDFEKRIP DPOB_HUMAN 136 55 -
RIGLKYFEDFEKRIP DPOB_RAT 136 55 -
KIGLKHFDDFEKRIP DPOB_XENLA 136 55 -
RVGIKYFYDINEKIP Q23687 140 58 -
LFGWSYYDDWLCKMS DPO4_YEAST 313 56 -

Motif 3 width=20
Element Seqn Id St Int Rpt
LQGSYNRGYSKCGDIDLLFF DPO4_YEAST 353 25 -
VCGSFRRGAESSGDMDVLLT DPOB_HUMAN 176 25 -
VCGSFRRGAESSGDMDVLLT DPOB_RAT 176 25 -
VCGSFRRGAESSGDMDILLT DPOB_XENLA 176 25 -
ISGTYRRRHPFSGDVDALLS Q23687 181 26 -

Motif 4 width=9
Element Seqn Id St Int Rpt
RRIDIRLIP DPOB_HUMAN 252 56 -
RRIDIRLIP DPOB_RAT 252 56 -
RRIDIRLIP DPOB_XENLA 251 55 -
RRVDIRLIE Q23687 268 67 -
RRLDFFCCK DPO4_YEAST 498 125 -

Motif 5 width=8
Element Seqn Id St Int Rpt
GVLYFTGS DPOB_HUMAN 267 6 -
GVLYFTGS DPOB_RAT 267 6 -
GVLYFTGS DPOB_XENLA 266 6 -
AMLTFTGS Q23687 283 6 -
GRIHYTGS DPO4_YEAST 513 6 -

Motif 6 width=18
Element Seqn Id St Int Rpt
EKDIFDYIQWKYREPKDR DPOB_HUMAN 315 40 -
EQDIFDYIQWRYREPKDR DPOB_RAT 315 40 -
EKDIFDYIQWKYREPKDR DPOB_XENLA 314 40 -
EQDVFDALGMPYAKPENR Q23687 357 66 -
ERRIFELLNLKYAEPEHR DPO4_YEAST 555 34 -