WORKLIST ENTRIES (1):
DNAPOLX View alignment View Structure DNA-polymerase family X signature
Type of fingerprint: COMPOUND with 6 elements
Links:
PRINTS; PR00106 DNAPOLB; PR00867 DNAPOLG; PR00868 DNAPOLI
PRINTS; PR00870 DNAPOLXBETA; PR00871 DNAPOLXTDT; PR00866 RNADNAPOLMS
INTERPRO; IPR002054
PROSITE; PS00522 DNA_POLYMERASE_X
PFAM; PF00966 DNA_polymeraseX
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].
DNAPOLX is a 6-element fingerprint that provides a signature for DNA-
polymerase family X. The fingerprint was derived from an initial alignment
of 8 sequences: the motifs were drawn from conserved regions spanning the
full alignment length - motif 1 includes helix 7 and a number of conserved
residues involved in metal and DNA binding; motif 2 straddles strands
2 and 3, and helix 12; motif 3 includes "motif C", which contains two of
the active site Asps; motif 4 spans strand 7 and helix 14, and corresponds
to "motif A", which includes an active site Asp; motif 5 spans the
C-terminus of helix 15 and the N-terminus of helix 16, and includes a
conserved aromatic residue involved in ligand binding; and motif 6, which
lies at the C-terminus, spans helices 17 and 18. Two iterations on OWL30.1
were required to reach convergence, at which point a true set comprising 16
sequences was identified. Several partial matches were also found, all of
which are non-vertebrate polymerase X family homologues.
An update on SPTR37_9f identified a true set of 13 sequences, and 6
partial matches.
SUMMARY INFORMATION
13 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
2 codes involving 3 elements
4 codes involving 2 elements
COMPOSITE FINGERPRINT INDEX
6| 13 13 13 13 13 13
5| 0 0 0 0 0 0
4| 0 0 0 0 0 0
3| 0 2 0 0 2 2
2| 0 3 2 1 1 1
--+-------------------------------
| 1 2 3 4 5 6
True positives..
TDT_MOUSE TDT_BOVIN TDT_MONDO TDT_HUMAN
TDT_CHICK TDT_AMBME TDT_XENLA TDT_ONCMY
DPOB_XENLA DPOB_HUMAN DPOB_RAT YA26_SCHPO
DPO4_YEAST
Subfamily: Codes involving 3 elements
Subfamily True positives..
O26650 Q23687
Subfamily: Codes involving 2 elements
Subfamily True positives..
P77987 O174_ASFB7 O67416
PROTEIN TITLES
TDT_MOUSE DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
TDT_BOVIN DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
TDT_MONDO DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
TDT_HUMAN DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
TDT_CHICK DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
TDT_AMBME DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
TDT_XENLA DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
TDT_ONCMY DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
DPOB_XENLA DNA POLYMERASE BETA (EC 2.7.7.7) - XENOPUS LAEVIS (AFRICAN C
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).
YA26_SCHPO HYPOTHETICAL DNA POLYMERASE BETA-LIKE PROTEIN C2F7.06C - SCH
DPO4_YEAST DNA POLYMERASE IV (EC 2.7.7.7) (POL IV) - SACCHAROMYCES CERE
O26650 DNA-DEPENDENT DNA POLYMERASE FAMILY X - METHANOBACTERIUM THE
Q23687 DNA POLYMERASE BETA - CRITHIDIA FASCICULATA.
P77987 DNA POLYMERASE FAMILY X (EC 2.7.7.7) (DNA-DIRECTED DNA POLYM
O174_ASFB7 DNA POLYMERASE BETA-LIKE PROTEIN - AFRICAN SWINE FEVER VIRUS
O67416 DNA POLYMERASE BETA FAMILY - AQUIFEX AEOLICUS.
SCAN HISTORY
OWL30_1 2 400 NSINGLE
SPTR37_9f 2 200 NSINGLE
INITIAL MOTIF SETS
DNAPOLX1 Length of motif = 18 Motif number = 1
DNA-polymerase family X motif I - 1
PCODE ST INT
GVGVKTSEKWFRMGLRTV TDT_CHICK 257 257
GVGLKTSEKWFRMGFRSL TDT_BOVIN 268 268
GVGLKTSEKWFRMGFRTL TDT_HUMAN 257 257
GVGLKTAEKWFRMGFRTL TDT_MOUSE 257 257
GVGASHAAEWYQKGWRTI YA26_SCHPO 271 271
GIGPAAARKFFDEGIKTL XLY15732 105 105
GIGPSAARKFVDEGIKTL DPOB_HUMAN 104 104
GIGPSAARKLVDEGIKTL DPOB_RAT 104 104
DNAPOLX2 Length of motif = 15 Motif number = 2
DNA-polymerase family X motif II - 1
PCODE ST INT
TITGGFRRGKKIGHD TDT_CHICK 329 54
TMTGGFRRGKKIGHD TDT_BOVIN 340 54
TMTGGFRRGKKMGHD TDT_HUMAN 329 54
TMTGGFRRGKMTGHD TDT_MOUSE 329 54
CLVGGFRRGKPVGAD YA26_SCHPO 341 52
TVCGSFRRGAESSGD XLY15732 176 53
TVCGSFRRGAESSGD DPOB_HUMAN 175 53
TVCGSFRRGAESSGD DPOB_RAT 175 53
DNAPOLX3 Length of motif = 9 Motif number = 3
DNA-polymerase family X motif III - 1
PCODE ST INT
DIDFLITSP TDT_CHICK 343 -1
DVDFLITSP TDT_BOVIN 354 -1
DVDFLITSP TDT_HUMAN 343 -1
DVDFLITSP TDT_MOUSE 343 -1
DVDMVLSPS YA26_SCHPO 355 -1
DMDILLTHP XLY15732 190 -1
DMDVLLTHP DPOB_HUMAN 189 -1
DMDVLLTHP DPOB_RAT 189 -1
DNAPOLX4 Length of motif = 10 Motif number = 4
DNA-polymerase family X motif IV - 1
PCODE ST INT
RVDLVITPFE TDT_CHICK 428 76
RVDLVMCPYE TDT_BOVIN 442 79
RVDLVLCPYE TDT_HUMAN 431 79
RVDLVMCPYD TDT_MOUSE 432 80
RVDIIVVPPA YA26_SCHPO 417 53
RIDIRLIPKD XLY15732 253 54
RIDIRLIPKD DPOB_HUMAN 253 55
RIDIRLIPKD DPOB_RAT 253 55
DNAPOLX5 Length of motif = 14 Motif number = 5
DNA-polymerase family X motif V - 1
PCODE ST INT
LGWTGSRQFGRDLR TDT_CHICK 444 6
LGWTGSRQFERDIR TDT_BOVIN 458 6
LGWTGSRFERDLRR TDT_HUMAN 447 6
LGWTGSRQFERDLR TDT_MOUSE 447 5
LGWSGGIFFLRDLK YA26_SCHPO 433 6
LYFTGSDIFNKNMR XLY15732 269 6
LYFTGSDIFNKNMR DPOB_HUMAN 269 6
LYFTGSDIFNKNMR DPOB_RAT 269 6
DNAPOLX6 Length of motif = 19 Motif number = 6
DNA-polymerase family X motif VI - 1
PCODE ST INT
SEEEIFAHLGLDYVEPWER TDT_CHICK 486 28
SEEEIFAHLGLDYIEPWER TDT_BOVIN 500 28
SEEEIFAHLGLDYIEPWER TDT_HUMAN 488 27
SEEEIFAHLGLDYIEPWER TDT_MOUSE 509 48
AEKDIFRYFSLEYIEPKFR YA26_SCHPO 485 38
SEKDIFDYIQWKYREPKDR XLY15732 314 31
SEKDIFDYIQWKYREPKDR DPOB_HUMAN 314 31
SEQDIFDYIQWRYREPKDR DPOB_RAT 314 31
FINAL MOTIF SETS
DNAPOLX1 Length of motif = 18 Motif number = 1
DNA-polymerase family X motif I - 2
PCODE ST INT
GVGLKTAEKWFRMGFRTL TDT_MOUSE 257 257
GVGLKTSEKWFRMGFRSL TDT_BOVIN 268 268
GVGLKTADKWYRMGFRTL TDT_MONDO 259 259
GVGLKTSEKWFRMGFRTL TDT_HUMAN 257 257
GVGVKTSEKWFRMGLRTV TDT_CHICK 257 257
GVGLRTAEKWHRLGIRTL TDT_AMBME 250 250
GVGLKTSDKWFRMGFRTL TDT_XENLA 253 253
GVGPKTAEKWYRRGLRSL TDT_ONCMY 248 248
GIGPAAARKFFDEGIKTL DPOB_XENLA 104 104
GIGPSAARKFVDEGIKTL DPOB_HUMAN 104 104
GIGPSAARKLVDEGIKTL DPOB_RAT 104 104
GVGASHAAEWYQKGWRTI YA26_SCHPO 271 271
GIGSEIAKRWNLLNFESF DPO4_YEAST 278 278
DNAPOLX2 Length of motif = 15 Motif number = 2
DNA-polymerase family X motif II - 2
PCODE ST INT
TMTGGFRRGKMTGHD TDT_MOUSE 329 54
TMTGGFRRGKKIGHD TDT_BOVIN 340 54
TITGGFRRGKEFGHD TDT_MONDO 331 54
TMTGGFRRGKKMGHD TDT_HUMAN 329 54
TITGGFRRGKKIGHD TDT_CHICK 329 54
TLTGGFRRGNKTGHD TDT_AMBME 322 54
TLTGGFRRGKKKGHD TDT_XENLA 325 54
ALTGGFRRGKEYGHD TDT_ONCMY 320 54
TVCGSFRRGAESSGD DPOB_XENLA 175 53
TVCGSFRRGAESSGD DPOB_HUMAN 175 53
TVCGSFRRGAESSGD DPOB_RAT 175 53
CLVGGFRRGKPVGAD YA26_SCHPO 341 52
ELQGSYNRGYSKCGD DPO4_YEAST 352 56
DNAPOLX3 Length of motif = 9 Motif number = 3
DNA-polymerase family X motif III - 2
PCODE ST INT
DVDFLITSP TDT_MOUSE 343 -1
DVDFLITSP TDT_BOVIN 354 -1
DVDFLITSP TDT_MONDO 345 -1
DVDFLITSP TDT_HUMAN 343 -1
DIDFLITSP TDT_CHICK 343 -1
DVDMLITSP TDT_AMBME 336 -1
DVDILITCA TDT_XENLA 339 -1
DVDFLLTMP TDT_ONCMY 334 -1
DMDILLTHP DPOB_XENLA 189 -1
DMDVLLTHP DPOB_HUMAN 189 -1
DMDVLLTHP DPOB_RAT 189 -1
DVDMVLSPS YA26_SCHPO 355 -1
DIDLLFFKP DPO4_YEAST 366 -1
DNAPOLX4 Length of motif = 10 Motif number = 4
DNA-polymerase family X motif IV - 2
PCODE ST INT
RVDLVMCPYD TDT_MOUSE 432 80
RVDLVMCPYE TDT_BOVIN 442 79
RVDLVVCPYD TDT_MONDO 440 86
RVDLVLCPYE TDT_HUMAN 431 79
RVDLVITPFE TDT_CHICK 428 76
RVDLVFCPFE TDT_AMBME 429 84
RLDLVITPYE TDT_XENLA 429 81
RVDLVAPPVD TDT_ONCMY 424 81
RIDIRLIPKD DPOB_XENLA 252 54
RIDIRLIPKD DPOB_HUMAN 253 55
RIDIRLIPKD DPOB_RAT 253 55
RVDIIVVPPA YA26_SCHPO 417 53
RLDFFCCKWD DPO4_YEAST 499 124
DNAPOLX5 Length of motif = 14 Motif number = 5
DNA-polymerase family X motif V - 2
PCODE ST INT
LGWTGSRQFERDLR TDT_MOUSE 447 5
LGWTGSRQFERDIR TDT_BOVIN 458 6
LGWSGSRQFERDLR TDT_MONDO 456 6
LGWTGSRFERDLRR TDT_HUMAN 447 6
LGWTGSRQFGRDLR TDT_CHICK 444 6
LGWTGSRQFERDLR TDT_AMBME 445 6
LGWTGSRQFERDLR TDT_XENLA 445 6
LGWTGSRFGRDLRT TDT_ONCMY 440 6
LYFTGSDIFNKNMR DPOB_XENLA 268 6
LYFTGSDIFNKNMR DPOB_HUMAN 269 6
LYFTGSDIFNKNMR DPOB_RAT 269 6
LGWSGGIFFLRDLK YA26_SCHPO 433 6
IHYTGSKEYNRWIR DPO4_YEAST 515 6
DNAPOLX6 Length of motif = 19 Motif number = 6
DNA-polymerase family X motif VI - 2
PCODE ST INT
SEEEIFAHLGLDYIEPWER TDT_MOUSE 509 48
SEEEIFAHLGLDYIEPWER TDT_BOVIN 500 28
SEEEIFAHLGLEYIQPSER TDT_MONDO 498 28
SEEEIFAHLGLDYIEPWER TDT_HUMAN 488 27
SEEEIFAHLGLDYVEPWER TDT_CHICK 486 28
SGEEIFGHLGLEYIDPVER TDT_AMBME 487 28
NEEDIFKQLGLDYLEPWER TDT_XENLA 487 28
TEEDIFTHLGLEYVEPWQR TDT_ONCMY 481 27
SEKDIFDYIQWKYREPKDR DPOB_XENLA 313 31
SEKDIFDYIQWKYREPKDR DPOB_HUMAN 314 31
SEQDIFDYIQWRYREPKDR DPOB_RAT 314 31
AEKDIFRYFSLEYIEPKFR YA26_SCHPO 485 38
NERRIFELLNLKYAEPEHR DPO4_YEAST 554 25
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