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PR00871

Identifier
DNAPOLXTDT  [View Relations]  [View Alignment]  
Accession
PR00871
No. of Motifs
10
Creation Date
29-JUN-1998  (UPDATE 07-JUN-1999)
Title
DNA nucleotidylexotransferase (TDT) signature
Database References
PRINTS; PR90005 DNADNAPOL; PR00869 DNAPOLX
INTERPRO; IPR001726
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]. 
 
DNAPOLXTDT is a 10-element fingerprint that provides a signature for the DNA
nucleotidylexotransferase (TDT) 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 TDT proteins but distinguish them from the polymerase X
and beta-like families - motif 8, which corresponds to "motif C", encodes
strand 7, which contains an active site Asp. Two iterations on OWL30.1 were 
required to reach convergence, at which point a true set comprising 9 
sequences was identified.
 
An update on SPTR37_9f identified a true set of 8 sequences.
Summary Information
8 codes involving 10 elements
0 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
108888888888
90000000000
80000000000
70000000000
60000000000
50000000000
40000000000
30000000000
20000000000
12345678910
True Positives
TDT_AMBME     TDT_BOVIN     TDT_CHICK     TDT_HUMAN     
TDT_MONDO TDT_MOUSE TDT_ONCMY TDT_XENLA
Sequence Titles
TDT_AMBME   DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITION ENZYME) (TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE) (TERMINAL TRANSFERASE) - AMBYSTOMA MEXICANUM (AXOLOTL). 
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_MONDO DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITION ENZYME) (TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE) (TDT) (TERMINAL TRANSFERASE) - MONODELPHIS DOMESTICA (SHORT-TAILED GREY OPOSSUM).
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).
Scan History
OWL30_1    2  50   NSINGLE    
SPTR37_9f 2 9 NSINGLE
Initial Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
RRTFLMELARSKGFRVE TDT_CHICK 48 48 -
RRAFLMELARRKGFRVE TDT_MOUSE 48 48 -
RRAFLMELARRKGFRVE TDT_HUMAN 48 48 -
RRNFLMELARRKGFRVE TDT_BOVIN 59 59 -
RRTFLTDLARKKGFRVE MDU91571 48 48 -
RRYFLMELARKKGFRVE AF039209 48 48 -
RRNFLTRLARSKGFRVE OMU53366 45 45 -

Motif 2 width=14
Element Seqn Id St Int Rpt
LSDSVTHIVAENNS TDT_HUMAN 67 2 -
LSDDVTHVVAEDNQ OMU53366 64 2 -
LSDSVTHIVAENNS TDT_BOVIN 78 2 -
LSDSVTHIVAENNS TDT_CHICK 67 2 -
LSNSVTHIVAENNS MDU91571 67 2 -
LSEYVTHVVSEKNS AF039209 67 2 -
LSDSVTHIVAENNS TDT_MOUSE 67 2 -

Motif 3 width=16
Element Seqn Id St Int Rpt
LDISWFTDSMREGRPV OMU53366 99 21 -
LDISWFTDRMGAGQPV AF039209 102 21 -
LDISWLTACMEMGRPV TDT_CHICK 102 21 -
LDISWLIECMGAGKPV TDT_MOUSE 102 21 -
LDVSWLIECIGAGKPV TDT_HUMAN 102 21 -
LDVSWLIESMGAGKPV TDT_BOVIN 113 21 -
LDISWLIECMKVGKPV MDU91571 102 21 -

Motif 4 width=16
Element Seqn Id St Int Rpt
FTDAFDILAENCEFRE TDT_HUMAN 168 50 -
FTDVMEELAESSEFNE OMU53366 159 44 -
FTDAFEILAKNYEFKE MDU91571 170 52 -
FTDAFEILAENYEFRE AF039209 164 46 -
FTDAFEILAENSEFKE TDT_BOVIN 179 50 -
FTDALDILAENDELRE TDT_MOUSE 168 50 -
FTDAFEIMAENYEFKE TDT_CHICK 168 50 -

Motif 5 width=13
Element Seqn Id St Int Rpt
FLRAASVLKSLPF TDT_CHICK 191 7 -
FRQAASVLKSLTF AF039209 187 7 -
FMRAISVLKCLPF MDU91571 193 7 -
FRQAASVLKSLPS OMU53366 182 7 -
FMRAASVLKSLPF TDT_BOVIN 202 7 -
FMRAASVLKSLPF TDT_HUMAN 191 7 -
FMRASSVLKSLPF TDT_MOUSE 191 7 -

Motif 6 width=12
Element Seqn Id St Int Rpt
PDAVVTLTGGFR AF039209 317 117 -
PDAFVTMTGGFR TDT_BOVIN 335 120 -
PDAFVTMTGGFR TDT_HUMAN 324 120 -
PDALVTITGGFR MDU91571 326 120 -
PDAILALTGGFR OMU53366 315 120 -
PDALVTMTGGFR TDT_MOUSE 324 120 -
PDALVTITGGFR TDT_CHICK 324 120 -

Motif 7 width=23
Element Seqn Id St Int Rpt
STMDEDNLPSKSVNLLDHFQKCF AF039209 374 45 -
STFDVSKLPSCRFEDMDCFQKCF OMU53366 372 45 -
STFEKFKLPSRQVDTLDHFQKCF TDT_BOVIN 393 46 -
STFVKEQIPSRHVDAMDHFQKCF TDT_CHICK 373 37 -
STFEKFKQPSRKVDALDHFQKCF TDT_MOUSE 383 47 -
STFEKLRLPSRKVDALDHFQKCF TDT_HUMAN 382 46 -
STFEDLKLPSRKIDALDHFQKCF MDU91571 385 47 -

Motif 8 width=12
Element Seqn Id St Int Rpt
WRAVRVDLVAPP OMU53366 420 25 -
WKAIRVDLVFCP AF039209 425 28 -
WKAIRVDLVVCP MDU91571 436 28 -
WKAIRVDLVMCP TDT_BOVIN 438 22 -
WKAIRVDLVLCP TDT_HUMAN 427 22 -
WKAIRVDLVMCP TDT_MOUSE 428 22 -
WKAIRVDLVITP TDT_CHICK 424 28 -

Motif 9 width=24
Element Seqn Id St Int Rpt
DLRTFAQKERQMLLDNHALYDKTK OMU53366 450 18 -
DLRRYATHEKKMMLDNHALYDKTK MDU91571 467 19 -
DLRRYASHEKKMMIDNHALYDKTK AF039209 456 19 -
DIRRYATHERKMMLDNHALYDKTK TDT_BOVIN 469 19 -
DLRRYATHERKMILDNHALYDKTK TDT_HUMAN 457 18 -
DLRRYATHERKMMLDNHALYDRTK TDT_MOUSE 458 18 -
DLRRYATHERKMMLDNHALYDKRK TDT_CHICK 455 19 -

Motif 10 width=20
Element Seqn Id St Int Rpt
EEEIFAHLGLDYIEPWERNA TDT_MOUSE 510 28 -
GEEIFGHLGLEYIDPVERNA AF039209 488 8 -
EEEIFAHLGLDYIEPWERNA TDT_BOVIN 501 8 -
EEEIFAHLGLDYIEPWERNA TDT_HUMAN 489 8 -
EEEIFAHLGLEYIQPSERNA MDU91571 499 8 -
EEDIFTHLGLEYVEPWQRNA OMU53366 482 8 -
EEEIFAHLGLDYVEPWERNA TDT_CHICK 487 8 -
Final Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
RRNFLMELARRKGFRVE TDT_BOVIN 59 59 -
RRAFLMELARRKGFRVE TDT_HUMAN 48 48 -
RRAFLMELARRKGFRVE TDT_MOUSE 48 48 -
RRTFLMELARSKGFRVE TDT_CHICK 48 48 -
RRTFLTDLARKKGFRVE TDT_MONDO 48 48 -
RRTFLMELARKRGFQTE TDT_XENLA 48 48 -
RRYFLMELARKKGFRVE TDT_AMBME 48 48 -
RRNFLTRLARSKGFRVE TDT_ONCMY 45 45 -

Motif 2 width=14
Element Seqn Id St Int Rpt
LSDSVTHIVAENNS TDT_BOVIN 78 2 -
LSDSVTHIVAENNS TDT_HUMAN 67 2 -
LSDSVTHIVAENNS TDT_MOUSE 67 2 -
LSDSVTHIVAENNS TDT_CHICK 67 2 -
LSNSVTHIVAENNS TDT_MONDO 67 2 -
LSDSVTHIVAENNS TDT_XENLA 67 2 -
LSEYVTHVVSEKNS TDT_AMBME 67 2 -
LSDDVTHVVAEDNQ TDT_ONCMY 64 2 -

Motif 3 width=16
Element Seqn Id St Int Rpt
LDVSWLIESMGAGKPV TDT_BOVIN 113 21 -
LDVSWLIECIGAGKPV TDT_HUMAN 102 21 -
LDISWLIECMGAGKPV TDT_MOUSE 102 21 -
LDISWLTACMEMGRPV TDT_CHICK 102 21 -
LDISWLIECMKVGKPV TDT_MONDO 102 21 -
LDISWFTECMEAGRPV TDT_XENLA 102 21 -
LDISWFTDRMGAGQPV TDT_AMBME 102 21 -
LDISWFTDSMREGRPV TDT_ONCMY 99 21 -

Motif 4 width=16
Element Seqn Id St Int Rpt
FTDAFEILAENSEFKE TDT_BOVIN 179 50 -
FTDAFDILAENCEFRE TDT_HUMAN 168 50 -
FTDALDILAENDELRE TDT_MOUSE 168 50 -
FTDAFEIMAENYEFKE TDT_CHICK 168 50 -
FTDAFEILAKNYEFKE TDT_MONDO 170 52 -
FTDAFDILAEHFEFCE TDT_XENLA 164 46 -
FTDAFEILAENYEFRE TDT_AMBME 164 46 -
FTDVMEELAESSEFNE TDT_ONCMY 159 44 -

Motif 5 width=13
Element Seqn Id St Int Rpt
FMRAASVLKSLPF TDT_BOVIN 202 7 -
FMRAASVLKSLPF TDT_HUMAN 191 7 -
FMRASSVLKSLPF TDT_MOUSE 191 7 -
FLRAASVLKSLPF TDT_CHICK 191 7 -
FMRAISVLKCLPF TDT_MONDO 193 7 -
FLRASSLIKSLPF TDT_XENLA 187 7 -
FRQAASVLKSLTF TDT_AMBME 187 7 -
FRQAASVLKSLPS TDT_ONCMY 182 7 -

Motif 6 width=12
Element Seqn Id St Int Rpt
PDAFVTMTGGFR TDT_BOVIN 335 120 -
PDAFVTMTGGFR TDT_HUMAN 324 120 -
PDALVTMTGGFR TDT_MOUSE 324 120 -
PDALVTITGGFR TDT_CHICK 324 120 -
PDALVTITGGFR TDT_MONDO 326 120 -
PDAIVTLTGGFR TDT_XENLA 320 120 -
PDAVVTLTGGFR TDT_AMBME 317 117 -
PDAILALTGGFR TDT_ONCMY 315 120 -

Motif 7 width=23
Element Seqn Id St Int Rpt
STFEKFKLPSRQVDTLDHFQKCF TDT_BOVIN 393 46 -
STFEKLRLPSRKVDALDHFQKCF TDT_HUMAN 382 46 -
STFEKFKQPSRKVDALDHFQKCF TDT_MOUSE 383 47 -
STFVKEQIPSRHVDAMDHFQKCF TDT_CHICK 373 37 -
STFEDLKLPSRKIDALDHFQKCF TDT_MONDO 385 47 -
STFDETKLPSRHVDALDHFQKCF TDT_XENLA 377 45 -
STMDEDNLPSKSVNLLDHFQKCF TDT_AMBME 374 45 -
STFDVSKLPSCRFEDMDCFQKCF TDT_ONCMY 372 45 -

Motif 8 width=12
Element Seqn Id St Int Rpt
WKAIRVDLVMCP TDT_BOVIN 438 22 -
WKAIRVDLVLCP TDT_HUMAN 427 22 -
WKAIRVDLVMCP TDT_MOUSE 428 22 -
WKAIRVDLVITP TDT_CHICK 424 28 -
WKAIRVDLVVCP TDT_MONDO 436 28 -
WKAVRLDLVITP TDT_XENLA 425 25 -
WKAIRVDLVFCP TDT_AMBME 425 28 -
WRAVRVDLVAPP TDT_ONCMY 420 25 -

Motif 9 width=24
Element Seqn Id St Int Rpt
DIRRYATHERKMMLDNHALYDKTK TDT_BOVIN 469 19 -
DLRRYATHERKMILDNHALYDKTK TDT_HUMAN 457 18 -
DLRRYATHERKMMLDNHALYDRTK TDT_MOUSE 458 18 -
DLRRYATHERKMMLDNHALYDKRK TDT_CHICK 455 19 -
DLRRYATHEKKMMLDNHALYDKTK TDT_MONDO 467 19 -
DLRRYATHEKRMMLDNHGLYDKTK TDT_XENLA 456 19 -
DLRRYASHEKKMMIDNHALYDKTK TDT_AMBME 456 19 -
DLRTFAQKERQMLLDNHALYDKTK TDT_ONCMY 450 18 -

Motif 10 width=20
Element Seqn Id St Int Rpt
EEEIFAHLGLDYIEPWERNA TDT_BOVIN 501 8 -
EEEIFAHLGLDYIEPWERNA TDT_HUMAN 489 8 -
EEEIFAHLGLDYIEPWERNA TDT_MOUSE 510 28 -
EEEIFAHLGLDYVEPWERNA TDT_CHICK 487 8 -
EEEIFAHLGLEYIQPSERNA TDT_MONDO 499 8 -
EEDIFKQLGLDYLEPWERNA TDT_XENLA 488 8 -
GEEIFGHLGLEYIDPVERNA TDT_AMBME 488 8 -
EEDIFTHLGLEYVEPWQRNA TDT_ONCMY 482 8 -