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. SPICER, E.K., RUSH, J., FUNG, C., REHA-KRANTZ, L.J., KARAM, J.D.
AND KONIGSBERG, W.H.
Primary structure of T4 DNA polymerase. Evolutionary relatedness to
eucaryotic and other procaryotic DNA polymerases.
J.BIOL.CHEM. 263 7478-7486 (1988).
|
Documentation | DNA is 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 life cycle of a cell. This function is performed by DNA-
directed DNA-polymerases by adding nucleotide triphosphate (dNTP) residues
to the 5'-end of the growing chain of DNA, using a complementary DNA chain
as a template. Small RNA molecules are generally used as primers for chain
elongation, although terminal proteins may also be used. Even though there
are 2 different methods of priming, these are mediated by 2 very similar
polymerases with similar methods of chain elongation.
There are 2 distinct classes of DNA-directed DNA-polymerase, A and B,
defined according to sequence similarity criteria. All sequences in the B
family contain a characteristic DTDS motif, and possess many functional
domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain,
a DNA binding domain, and binding domains for both dNTP's and pyrophosphate.
DNAPOLB is a 3-element fingerprint that provides a signature for class
B polymerases. The fingerprint was derived from an initial alignment of 5
sequences: the motifs correspond to the conserved regions described by
Jung et al. [1], motif 3 containing the DTDS motif, which is universally
conserved in B DNA-polymerases (cf. PROSITE pattern DNA_POLYMERASE_B).
Three iterations on OWL12.0 were required to reach convergence, at which
point a true set comprising 40 sequences was identified. Three partial
matches were also found: of these, all are family members, but 2 (HS5DNAPOL
and S06416) are truncated sequences, HS5DNAPOL ending just after the
C-terminus of the second motif, and S06416 lacking the first motif;
DPO2_KLULA is a complete sequence, but fails to make a significant match
with motif 2.
An update on SPTR37_9f identified a true set of 134 sequences, and 10
partial matches.
|
Sequence Titles | DPO1_KLULA DNA POLYMERASE (EC 2.7.7.7) - KLUYVEROMYCES LACTIS (YEAST). DPO1_SULOH DNA POLYMERASE I (EC 2.7.7.7) (DNA POLYMERASE B1) - SULFURISPHAERA OHWAKUENSIS. DPO1_SULSO DNA POLYMERASE I (EC 2.7.7.7) - SULFOLOBUS SOLFATARICUS. DPO2_ECOLI DNA POLYMERASE II (EC 2.7.7.7) (POL II) - ESCHERICHIA COLI. DPOA_DROME DNA POLYMERASE ALPHA CATALYTIC SUBUNIT (EC 2.7.7.7) - DROSOPHILA MELANOGASTER (FRUIT FLY). DPOA_HUMAN DNA POLYMERASE ALPHA CATALYTIC SUBUNIT (EC 2.7.7.7) - HOMO SAPIENS (HUMAN). DPOA_LEIDO DNA POLYMERASE ALPHA CATALYTIC SUBUNIT (EC 2.7.7.7) - LEISHMANIA DONOVANI. DPOA_MOUSE DNA POLYMERASE ALPHA CATALYTIC SUBUNIT (EC 2.7.7.7) - MUS MUSCULUS (MOUSE). DPOA_ORYSA DNA POLYMERASE ALPHA CATALYTIC SUBUNIT (EC 2.7.7.7) - ORYZA SATIVA (RICE). DPOA_OXYNO DNA POLYMERASE ALPHA CATALYTIC SUBUNIT (EC 2.7.7.7) - OXYTRICHA NOVA. DPOA_OXYTR DNA POLYMERASE ALPHA CATALYTIC SUBUNIT (EC 2.7.7.7) - OXYTRICHA TRIFALLAX. DPOA_SCHPO DNA POLYMERASE ALPHA CATALYTIC SUBUNIT (EC 2.7.7.7) (DNA POLYMERASE I) - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST). DPOA_TRYBB DNA POLYMERASE ALPHA CATALYTIC SUBUNIT (EC 2.7.7.7) (DNA POLYMERASE I) - TRYPANOSOMA BRUCEI BRUCEI. DPOA_YEAST DNA POLYMERASE ALPHA CATALYTIC SUBUNIT (EC 2.7.7.7) (DNA POLYMERASE I) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). DPOD_BOVIN DNA POLYMERASE DELTA CATALYTIC CHAIN (EC 2.7.7.7) - BOS TAURUS (BOVINE). DPOD_CANAL DNA POLYMERASE DELTA LARGE CHAIN (EC 2.7.7.7) (DNA POLYMERASE III) - CANDIDA ALBICANS (YEAST). DPOD_DROME DNA POLYMERASE DELTA CATALYTIC CHAIN (EC 2.7.7.7) - DROSOPHILA MELANOGASTER (FRUIT FLY). DPOD_HUMAN DNA POLYMERASE DELTA CATALYTIC CHAIN (EC 2.7.7.7) - HOMO SAPIENS (HUMAN). DPOD_MESAU DNA POLYMERASE DELTA CATALYTIC CHAIN (EC 2.7.7.7) - MESOCRICETUS AURATUS (GOLDEN HAMSTER). DPOD_MOUSE DNA POLYMERASE DELTA CATALYTIC CHAIN (EC 2.7.7.7) - MUS MUSCULUS (MOUSE). DPOD_PLAFK DNA POLYMERASE DELTA CATALYTIC CHAIN (EC 2.7.7.7) - PLASMODIUM FALCIPARUM (ISOLATE K1 / THAILAND). DPOD_RAT DNA POLYMERASE DELTA CATALYTIC CHAIN (EC 2.7.7.7) - RATTUS NORVEGICUS (RAT). DPOD_SCHPO DNA POLYMERASE DELTA LARGE CHAIN (EC 2.7.7.7) (DNA POLYMERASE III) - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST). DPOD_SOYBN DNA POLYMERASE DELTA CATALYTIC CHAIN (EC 2.7.7.7) - GLYCINE MAX (SOYBEAN). DPOD_YEAST DNA POLYMERASE DELTA LARGE CHAIN (EC 2.7.7.7) (DNA POLYMERASE III) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). DPOE_HUMAN DNA POLYMERASE EPSILON, CATALYTIC SUBUNIT A (EC 2.7.7.7) (DNA POLYMERASE II SUBUNIT A) - HOMO SAPIENS (HUMAN). DPOE_SCHPO DNA POLYMERASE EPSILON, CATALYTIC SUBUNIT A (EC 2.7.7.7) (DNA POLYMERASE II SUBUNIT A) - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST). DPOE_YEAST DNA POLYMERASE EPSILON, CATALYTIC SUBUNIT A (EC 2.7.7.7) (DNA POLYMERASE II SUBUNIT A) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). DPOL_ADE02 DNA POLYMERASE (EC 2.7.7.7) - HUMAN ADENOVIRUS TYPE 2. DPOL_ADE04 DNA POLYMERASE (EC 2.7.7.7) - HUMAN ADENOVIRUS TYPE 4. DPOL_ADE05 DNA POLYMERASE (EC 2.7.7.7) - HUMAN ADENOVIRUS TYPE 5. DPOL_ADE07 DNA POLYMERASE (EC 2.7.7.7) - HUMAN ADENOVIRUS TYPE 7. DPOL_ADE12 DNA POLYMERASE (EC 2.7.7.7) - HUMAN ADENOVIRUS TYPE 12. DPOL_ADE40 DNA POLYMERASE (EC 2.7.7.7) - HUMAN ADENOVIRUS TYPE 40. DPOL_ADEB2 DNA POLYMERASE (EC 2.7.7.7) - BOVINE ADENOVIRUS TYPE 2 (MASTADENOVIRUS BOS2). DPOL_ADEB3 DNA POLYMERASE (EC 2.7.7.7) - BOVINE ADENOVIRUS TYPE 3 (MASTADENOVIRUS BOS3). DPOL_ADECC DNA POLYMERASE (EC 2.7.7.7) - CANINE ADENOVIRUS TYPE 1 (STRAIN CLL). DPOL_ADECT DNA POLYMERASE (EC 2.7.7.7) - CANINE ADENOVIRUS TYPE 2 (STRAIN TORONTO A 26-61). DPOL_ADEG1 DNA POLYMERASE (EC 2.7.7.7) - AVIAN ADENOVIRUS GAL1 (STRAIN PHELPS) (FOWL ADENOVIRUS 1) (CELO). DPOL_ARCFU DNA POLYMERASE (EC 2.7.7.7) - ARCHAEOGLOBUS FULGIDUS. DPOL_ASFB7 DNA POLYMERASE (EC 2.7.7.7) - AFRICAN SWINE FEVER VIRUS (STRAIN BA71V) (ASFV). DPOL_ASFL6 DNA POLYMERASE (EC 2.7.7.7) - AFRICAN SWINE FEVER VIRUS (ISOLATE LISBON 60 / LIS60) (ASFV). DPOL_BPB03 DNA POLYMERASE (EC 2.7.7.7) (EARLY PROTEIN GP2) - BACTERIOPHAGE B103. DPOL_BPM2 DNA POLYMERASE (EC 2.7.7.7) - BACTERIOPHAGE M2. DPOL_BPPH2 DNA POLYMERASE (EC 2.7.7.7) (EARLY PROTEIN GP2) - BACTERIOPHAGE PHI-29. DPOL_BPPRD DNA POLYMERASE (EC 2.7.7.7) (PROTEIN P1) - BACTERIOPHAGE PRD1. DPOL_BPPZA DNA POLYMERASE (EC 2.7.7.7) (EARLY PROTEIN GP2) - BACTERIOPHAGE PZA. DPOL_BPR69 DNA POLYMERASE (EC 2.7.7.7) (GP43) - BACTERIOPHAGE RB69. DPOL_BPT4 DNA POLYMERASE (EC 2.7.7.7) (GP43) - BACTERIOPHAGE T4. DPOL_CBEPV DNA POLYMERASE (EC 2.7.7.7) - CHORISTONEURA BIENNIS ENTOMOPOXVIRUS (CBEPV). DPOL_CHVN2 DNA POLYMERASE (EC 2.7.7.7) - CHLORELLA VIRUS NY-2A (CV-NY2A). DPOL_CHVP1 DNA POLYMERASE (EC 2.7.7.7) - PARAMECIUM BURSARIA CHLORELLA VIRUS 1 (PBCV-1). DPOL_EBV DNA POLYMERASE (EC 2.7.7.7) - EPSTEIN-BARR VIRUS (STRAIN B95-8) (HUMAN HERPESVIRUS 4). DPOL_FOWPV DNA POLYMERASE (EC 2.7.7.7) - FOWLPOX VIRUS. DPOL_GPCMV DNA POLYMERASE (EC 2.7.7.7) - GUINEA PIG CYTOMEGALOVIRUS (STRAIN 22122 / ATCC VR682) (GPCMV). DPOL_HCMVA DNA POLYMERASE (EC 2.7.7.7) - HUMAN CYTOMEGALOVIRUS (STRAIN AD169). DPOL_HSV11 DNA POLYMERASE (EC 2.7.7.7) - HERPES SIMPLEX VIRUS (TYPE 1 / STRAIN 17). DPOL_HSV1A DNA POLYMERASE (EC 2.7.7.7) - HERPES SIMPLEX VIRUS (TYPE 1 / STRAIN ANGELOTTI). DPOL_HSV1K DNA POLYMERASE (EC 2.7.7.7) - HERPES SIMPLEX VIRUS (TYPE 1 / STRAIN KOS). DPOL_HSV1S DNA POLYMERASE (EC 2.7.7.7) - HERPES SIMPLEX VIRUS (TYPE 1 / STRAIN SC16). DPOL_HSV21 DNA POLYMERASE (EC 2.7.7.7) - HERPES SIMPLEX VIRUS (TYPE 2 / STRAIN 186). DPOL_HSV6U DNA POLYMERASE (EC 2.7.7.7) - HERPES SIMPLEX VIRUS (TYPE 6 / STRAIN UGANDA-1102). DPOL_HSV7J DNA POLYMERASE (EC 2.7.7.7) - HERPES SIMPLEX VIRUS (TYPE 7 / STRAIN JI) (HHV7). DPOL_HSVE2 DNA POLYMERASE (EC 2.7.7.7) - EQUINE HERPESVIRUS TYPE 2 (STRAIN 86/87) (EHV-2). DPOL_HSVEB DNA POLYMERASE (EC 2.7.7.7) - EQUINE HERPESVIRUS TYPE 1 (STRAIN AB4P) (EHV-1). DPOL_HSVI1 DNA POLYMERASE (EC 2.7.7.7) - ICTALURID HERPESVIRUS 1 (CHANNEL CATFISH VIRUS) (CCV). DPOL_HSVSA DNA POLYMERASE (EC 2.7.7.7) - HERPESVIRUS SAIMIRI (STRAIN 11). DPOL_MCMVS DNA POLYMERASE (EC 2.7.7.7) - MURINE CYTOMEGALOVIRUS (STRAIN SMITH). DPOL_METJA DNA POLYMERASE (EC 2.7.7.7) - METHANOCOCCUS JANNASCHII. DPOL_METTH DNA POLYMERASE (EC 2.7.7.7) - METHANOBACTERIUM THERMOAUTOTROPHICUM. DPOL_METVO DNA POLYMERASE (EC 2.7.7.7) - METHANOCOCCUS VOLTAE. DPOL_NPVAC DNA POLYMERASE (EC 2.7.7.7) - AUTOGRAPHA CALIFORNICA NUCLEAR POLYHEDROSIS VIRUS (ACMNPV). DPOL_NPVBM DNA POLYMERASE (EC 2.7.7.7) - BOMBYX MORI NUCLEAR POLYHEDROSIS VIRUS (BMNPV). DPOL_NPVCF DNA POLYMERASE (EC 2.7.7.7) - CHORISTONEURA FUMIFERANA NUCLEAR POLYHEDROSIS VIRUS (CFMNPV). DPOL_NPVLD DNA POLYMERASE (EC 2.7.7.7) - LYMANTRIA DISPAR MULTICAPSID NUCLEAR POLYHEDROSIS VIRUS (LDMNPV). DPOL_NPVOP DNA POLYMERASE (EC 2.7.7.7) - ORGYIA PSEUDOTSUGATA MULTICAPSID POLYHEDROSIS VIRUS (OPMNPV). DPOL_ORFN2 DNA POLYMERASE (EC 2.7.7.7) - ORF VIRUS (STRAIN NZ2) (OV NZ-2). DPOL_PYRAB DNA POLYMERASE (EC 2.7.7.7) (PAB POLYMERASE) - PYROCOCCUS ABYSSI. DPOL_PYRFU DNA POLYMERASE (EC 2.7.7.7) (PFU POLYMERASE) - PYROCOCCUS FURIOSUS, AND PYROCOCCUS WOESEI. DPOL_PYRHO DNA POLYMERASE (EC 2.7.7.7) - PYROCOCCUS HORIKOSHII. DPOL_PYRSD DNA POLYMERASE (EC 2.7.7.7) (DEEP VENT DNA POLYMERASE) [CONTAINS: PI-PSP I ENDONUCLEASE] - PYROCOCCUS SP. (STRAIN GB-D). DPOL_PYRSE DNA POLYMERASE (EC 2.7.7.7) - PYROCOCCUS SP. (STRAIN GE23). DPOL_RCMVM DNA POLYMERASE (EC 2.7.7.7) - RAT CYTOMEGALOVIRUS (STRAIN MAASTRICHT). DPOL_RHCM6 DNA POLYMERASE (EC 2.7.7.7) - RHESUS CYTOMEGALOVIRUS (STRAIN 68-1) (RHCMV). DPOL_RSIV DNA POLYMERASE (EC 2.7.7.7) - RED SEA BREAM IRIDOVIRUS (RSIV). DPOL_SULAC DNA POLYMERASE I (EC 2.7.7.7) - SULFOLOBUS ACIDOCALDARIUS. DPOL_THES9 DNA POLYMERASE (EC 2.7.7.7) - THERMOCOCCUS SP. (STRAIN 9ON-7). DPOL_VACCC DNA POLYMERASE (EC 2.7.7.7) - VACCINIA VIRUS (STRAIN COPENHAGEN). DPOL_VACCV DNA POLYMERASE (EC 2.7.7.7) - VACCINIA VIRUS (STRAIN WR). DPOL_VARV DNA POLYMERASE (EC 2.7.7.7) - VARIOLA VIRUS. DPOL_VZVD DNA POLYMERASE (EC 2.7.7.7) - VARICELLA-ZOSTER VIRUS (STRAIN DUMAS) (VZV). DPOM_CLAPU PROBABLE DNA POLYMERASE (EC 2.7.7.7) - CLAVICEPS PURPUREA (ERGOT FUNGUS). DPOM_MAIZE DNA POLYMERASE (EC 2.7.7.7) (S-1 DNA ORF 3) - ZEA MAYS (MAIZE). DPOM_NEUCR PROBABLE DNA POLYMERASE (EC 2.7.7.7) - NEUROSPORA CRASSA. DPOM_NEUIN PROBABLE DNA POLYMERASE (EC 2.7.7.7) - NEUROSPORA INTERMEDIA. DPOM_PODAN PROBABLE DNA POLYMERASE (EC 2.7.7.7) - PODOSPORA ANSERINA. DPOZ_HUMAN DNA POLYMERASE ZETA CATALYTIC SUBUNIT (EC 2.7.7.7) - HOMO SAPIENS (HUMAN). DPOZ_YEAST DNA POLYMERASE ZETA CATALYTIC SUBUNIT (EC 2.7.7.7) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). O03684 PROBABLE DNA POLYMERASE (EC 2.7.7.7) - GELASINOSPORA SP. O11414 DNA POLYMERASE - AVIAN ADENOVIRUS EDS. O36363 DNA POLYMERASE (EC 2.7.7.7) - ALCELAPHINE HERPESVIRUS 1 (WILDEBEEST HERPESVIRUS). O36638 DNA-DEPENDENT DNA POLYMERASE HOMOLOG (EC 2.7.7.7) - FELDMANNIA SP. VIRUS. O39234 DNA POLYMERASE (EC 2.7.7.7) - RHESUS MONKEY RHADINOVIRUS H26-95. O39272 COUNTERPART OF HSV-1 GENE UL30 AND VZV GENE 28 (EC 2.7.7.7) - EQUINE HERPESVIRUS 4. O40915 ORF 09 (EC 2.7.7.7) - KAPOSI'S SARCOMA-ASSOCIATED HERPESVIRUS (KSHV) (HUMAN HERPESVIRUS 8). O41930 DNA POLYMERASE (EC 2.7.7.7) - MURINE HERPESVIRUS 68. O57191 DNA POLYMERASE (EC 2.7.7.7) - VACCINIA VIRUS. O62074 C25F9.2 PROTEIN - CAENORHABDITIS ELEGANS. O62218 F33H2.5 PROTEIN - CAENORHABDITIS ELEGANS. O64795 T1F15.3 PROTEIN (EC 2.7.7.7) - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS). O74046 ARCHAEL FAMILY B DNA POLYMERASE (EC 2.7.7.7) - CENARCHAEUM SYMBIOSUM. O74719 DNA POLYMERASE (EC 2.7.7.7) - DEBARYOMYCES HANSENII (YEAST) (TORULASPORA HANSENII). O77034 DNA POLYMERASE ALPHA 180K SUBUNIT (EC 2.7.7.7) - DROSOPHILA MELANOGASTER (FRUIT FLY). O78938 B TYPE DNA POLYMERASE - AGROCYBE AEGERITA. O92787 DNA POLYMERASE - BOVINE ADENOVIRUS TYPE 3 (MASTADENOVIRUS BOS3). O92827 CATALYTIC SUBUNIT OF REPLICATIVE DNA POLYMERASE (EC 2.7.7.7) - HUMAN HERPESVIRUS 7. O93043 DNA POLYMERASE (EC 2.7.7.7) - FELINE HERPESVIRUS (FELID HERPESVIRUS 1). P77933 DNA-DEPENDENT DNA POLYMERASE (EC 2.7.7.7) (DNA-DIRECTED DNA POLYMERASE) (DNA NUCLEOTIDYLTRANSFERASE (DNA-DIRECTED)) - PYROCOCCUS SP. P88907 ORF 9 (EC 2.7.7.7) - KAPOSI'S SARCOMA-ASSOCIATED HERPESVIRUS (KSHV) (HUMAN HERPESVIRUS 8). P89285 DNA POLYMERASE HOMOLOG (EC 2.7.7.7) - XESTIA C-NIGRUM GRANULOSIS VIRUS (XNGV) (XESTIA C-NIGRUM GRANULOVIRUS). P89453 DNA POLYMERASE (EC 2.7.7.7) - HERPES SIMPLEX VIRUS (TYPE 2). P90829 F10C2.4 PROTEIN (EC 2.7.7.7) - CAENORHABDITIS ELEGANS. Q01140 PUTATIVE DNA-POLYMERASE, B-TYPE. Q35599 DNA POLYMERASE - PHYSARUM POLYCEPHALUM (SLIME MOLD). Q37989 DNA POLYMERASE - BACTERIOPHAGE CP-1. Q38545 BACTERIOPHAGE PHI29 TEMPERATURE SENSITIVE MUTANT TS2(98) DNA POLYMERASE - BACTERIOPHAGE PHI-29. Q59690 DNA POLYMERASE (EC 2.7.7.7) - PYRODICTIUM OCCULTUM. Q59691 DNA POLYMERASE (EC 2.7.7.7) - PYRODICTIUM OCCULTUM. Q69281 DNA POLYMERASE (EC 2.7.7.7) - TURKEY HERPESVIRUS. Q82482 DNA-DIRECTED DNA POLYMERASE - HELICOVERPA ZEA NUCLEAR POLYHEDROSIS VIRUS. Q86992 DNA POLYMERASE - SPODOPTERA ASCOVIRUS. Q89604 UL30 (EC 2.7.7.7) - BOVINE HERPESVIRUS 1. Q96206 DNA POLYMERASE - BACTERIOPHAGE GA. Q98207 MC039L (EC 2.7.7.7) - MOLLUSCUM CONTAGIOSUM VIRUS SUBTYPE 1 (MCVI). DPO2_KLULA DNA POLYMERASE (EC 2.7.7.7) (PLASMID PGKL-2 PROTEIN 2) - KLUYVEROMYCES LACTIS (YEAST). DPOL_THEFM DNA POLYMERASE (EC 2.7.7.7) (POL TFU) - THERMOCOCCUS FUMICOLANS. DPOL_THELI DNA POLYMERASE (EC 2.7.7.7) (VENT DNA POLYMERASE) [CONTAINS: PI-TLI I ENDONUCLEASE; PI-TLI II ENDONUCLEASE] - THERMOCOCCUS LITORALIS. DPOL_THEST DNA POLYMERASE (EC 2.7.7.7) - THERMOCOCCUS SP. (STRAIN TY). DPOM_ASCIM PROBABLE DNA POLYMERASE (EC 2.7.7.7) - ASCOBOLUS IMMERSUS. O21376 DNA POLYMERASE - PICHIA KLUYVERI (YEAST). O61796 C33E10.6 PROTEIN - CAENORHABDITIS ELEGANS. Q09038 SIMILARITY TO DNA POLYMERASE - SACCHAROMYCES KLUYVERI (YEAST). Q35590 ORF-221 - PHYSARUM POLYCEPHALUM (SLIME MOLD). Q39432 DNA POLYMERASE RELLATED DPO-R - BETA VULGARIS (SUGAR BEET).
|