WORKLIST ENTRIES (1):
DNAPOLXBETA View alignment View Structure DNA-polymerase family X pol beta-like signature
Type of fingerprint: COMPOUND with 6 elements
Links:
PRINTS; PR00106 DNAPOLB; PR00867 DNAPOLG; PR00868 DNAPOLI
PRINTS; PR00869 DNAPOLX; PR00871 DNAPOLXTDT; PR00866 RNADNAPOLMS
INTERPRO; IPR002008
PDB; 1BPY 3Dinfo; 1BPX 3Dinfo
SCOP; 1BPY; 1BPX
CATH; 1BPY; 1BPX
Creation date 29-JUN-1998; UPDATE 14-JUN-1999
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).
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
11 codes involving 2 elements
COMPOSITE FINGERPRINT INDEX
6| 5 5 5 5 5 5
5| 0 0 0 0 0 0
4| 1 0 1 0 1 1
3| 0 0 0 0 0 0
2| 2 1 9 1 1 8
--+-------------------------------
| 1 2 3 4 5 6
True positives..
DPOB_HUMAN DPOB_RAT DPOB_XENLA Q23687
DPO4_YEAST
Subfamily: Codes involving 4 elements
Subfamily True positives..
O26650
Subfamily: Codes involving 2 elements
Subfamily True positives..
CLPC_ODOSI P77987 O67416 TDT_HUMAN
TDT_ONCMY YA26_SCHPO TDT_XENLA TDT_CHICK
TDT_BOVIN TDT_MOUSE
PROTEIN TITLES
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 C
Q23687 DNA POLYMERASE BETA - CRITHIDIA FASCICULATA.
DPO4_YEAST DNA POLYMERASE IV (EC 2.7.7.7) (POL IV) - SACCHAROMYCES CERE
O26650 DNA-DEPENDENT DNA POLYMERASE FAMILY X - METHANOBACTERIUM THE
CLPC_ODOSI ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA HOMOLOG
P77987 DNA POLYMERASE FAMILY X (EC 2.7.7.7) (DNA-DIRECTED DNA POLYM
O67416 DNA POLYMERASE BETA FAMILY - AQUIFEX AEOLICUS.
TDT_ONCMY DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
YA26_SCHPO HYPOTHETICAL DNA POLYMERASE BETA-LIKE PROTEIN C2F7.06C - SCH
TDT_XENLA DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
TDT_CHICK DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
TDT_BOVIN DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
TDT_MOUSE DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
TDT_HUMAN DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
SCAN HISTORY
OWL30_1 2 500 NSINGLE
SPTR37_9f 2 100 NSINGLE
INITIAL MOTIF SETS
DNAPOLXBETA1 Length of motif = 18 Motif number = 1
DNA-polymerase family X (pol beta-like) motif I - 1
PCODE ST INT
NIGPSIAKKIQVILDTGV DPO4_YEAST 239 239
GVGTKIAEKIDEFLATGK DPOB_RAT 63 63
GVGTKIAEKIDEFLATGK DPOB_HUMAN 63 63
GVGAKIAEKIDEFLATGK XLY15732 64 64
GVGTKIAEKIDEFLATGK HUMPOLB 64 64
GVGTKIAEKIDEFLATGK RATPOLB1 64 64
GFGAKLLKKAEEIMATGK A55874 64 64
DNAPOLXBETA2 Length of motif = 15 Motif number = 2
DNA-polymerase family X (pol beta-like) motif II - 1
PCODE ST INT
LFGWSYYDDWLCKMS DPO4_YEAST 313 56
RIGLKYFEDFEKRIP DPOB_RAT 136 55
RIGLKYFGDFEKRIP DPOB_HUMAN 136 55
KIGLKHFDDFEKRIP XLY15732 137 55
RIGLKYFGDFEKRIP HUMPOLB 137 55
RIGLKYFEDFEKRIP RATPOLB1 137 55
RVGIKYFYDINEKIP A55874 140 58
DNAPOLXBETA3 Length of motif = 20 Motif number = 3
DNA-polymerase family X (pol beta-like) motif III - 1
PCODE ST INT
LQGSYNRGYSKCGDIDLLFF DPO4_YEAST 353 25
VCGSFRRGAESSGDMDVLLT DPOB_RAT 176 25
VCGSFRRGAESSGDMDVLLT DPOB_HUMAN 176 25
VCGSFRRGAESSGDMDILLT XLY15732 177 25
VCGSFRRGAESSGDMDVLLT HUMPOLB 177 25
VCGSFRRGAESSGDMDVLLT RATPOLB1 177 25
ISGTYRRRHPFSGDVDALLS A55874 181 26
DNAPOLXBETA4 Length of motif = 9 Motif number = 4
DNA-polymerase family X (pol beta-like) motif IV - 1
PCODE ST INT
RRLDFFCCK DPO4_YEAST 498 125
RRIDIRLIP DPOB_RAT 252 56
RRIDIRLIP DPOB_HUMAN 252 56
RRIDIRLIP XLY15732 252 55
RRIDIRLYP HUMPOLB 253 56
RRIDIRLIP RATPOLB1 253 56
RRVDIRLIE A55874 268 67
DNAPOLXBETA5 Length of motif = 8 Motif number = 5
DNA-polymerase family X (pol beta-like) motif V - 1
PCODE ST INT
GRIHYTGS DPO4_YEAST 513 6
GVLYFTGS DPOB_RAT 267 6
GVLYFTGS DPOB_HUMAN 267 6
GVLYFTGS XLY15732 267 6
GVLYFTGS HUMPOLB 268 6
GVLYFTGS RATPOLB1 268 6
AMLTFTGS A55874 283 6
DNAPOLXBETA6 Length of motif = 18 Motif number = 6
DNA-polymerase family X (pol beta-like) motif VI - 1
PCODE ST INT
ERRIFELLNLKYAEPEHR DPO4_YEAST 555 34
EQDIFDYIQWRYREPKDR DPOB_RAT 315 40
EKDIFDYIQWKYREPKDR DPOB_HUMAN 315 40
EKDIFDYIQWKYREPKDR XLY15732 315 40
EKDIFDYIQWKYREPKDR HUMPOLB 316 40
EQDIFDYIQWRYREPKDR RATPOLB1 316 40
EQDVFDALGMPYAKPENR A55874 357 66
FINAL MOTIF SETS
DNAPOLXBETA1 Length of motif = 18 Motif number = 1
DNA-polymerase family X (pol beta-like) motif I - 2
PCODE ST INT
GVGTKIAEKIDEFLATGK DPOB_HUMAN 63 63
GVGTKIAEKIDEFLATGK DPOB_RAT 63 63
GVGAKIAEKIDEFLATGK DPOB_XENLA 63 63
GFGAKLLKKAEEIMATGK Q23687 64 64
NIGPSIAKKIQVILDTGV DPO4_YEAST 239 239
DNAPOLXBETA2 Length of motif = 15 Motif number = 2
DNA-polymerase family X (pol beta-like) motif II - 2
PCODE ST INT
RIGLKYFGDFEKRIP DPOB_HUMAN 136 55
RIGLKYFEDFEKRIP DPOB_RAT 136 55
KIGLKHFDDFEKRIP DPOB_XENLA 136 55
RVGIKYFYDINEKIP Q23687 140 58
LFGWSYYDDWLCKMS DPO4_YEAST 313 56
DNAPOLXBETA3 Length of motif = 20 Motif number = 3
DNA-polymerase family X (pol beta-like) motif III - 2
PCODE ST INT
VCGSFRRGAESSGDMDVLLT DPOB_HUMAN 176 25
VCGSFRRGAESSGDMDVLLT DPOB_RAT 176 25
VCGSFRRGAESSGDMDILLT DPOB_XENLA 176 25
ISGTYRRRHPFSGDVDALLS Q23687 181 26
LQGSYNRGYSKCGDIDLLFF DPO4_YEAST 353 25
DNAPOLXBETA4 Length of motif = 9 Motif number = 4
DNA-polymerase family X (pol beta-like) motif IV - 2
PCODE ST INT
RRIDIRLIP DPOB_HUMAN 252 56
RRIDIRLIP DPOB_RAT 252 56
RRIDIRLIP DPOB_XENLA 251 55
RRVDIRLIE Q23687 268 67
RRLDFFCCK DPO4_YEAST 498 125
DNAPOLXBETA5 Length of motif = 8 Motif number = 5
DNA-polymerase family X (pol beta-like) motif V - 2
PCODE ST INT
GVLYFTGS DPOB_HUMAN 267 6
GVLYFTGS DPOB_RAT 267 6
GVLYFTGS DPOB_XENLA 266 6
AMLTFTGS Q23687 283 6
GRIHYTGS DPO4_YEAST 513 6
DNAPOLXBETA6 Length of motif = 18 Motif number = 6
DNA-polymerase family X (pol beta-like) motif VI - 2
PCODE ST INT
EKDIFDYIQWKYREPKDR DPOB_HUMAN 315 40
EQDIFDYIQWRYREPKDR DPOB_RAT 315 40
EKDIFDYIQWKYREPKDR DPOB_XENLA 314 40
EQDVFDALGMPYAKPENR Q23687 357 66
ERRIFELLNLKYAEPEHR DPO4_YEAST 555 34
User query: Display/Full Code "DNAPOLXBETA"