1S5J,1Q8I,1QHT,1CLQ


Conserved Protein Domain Family
DEDDy_DNA_polB_exo

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cd05160: DEDDy_DNA_polB_exo 
Click on image for an interactive view with Cn3D
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases
The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon and zeta), and eukaryotic viral and plasmid-borne enzymes. Nuclear DNA polymerases alpha and zeta lack the four conserved acidic metal-binding residues. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Statistics
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PSSM-Id: 176646
Aligned: 20 rows
Threshold Bit Score: 161.754
Created: 26-Apr-2007
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 13 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Comment:The active site includes the catalytic site (characterized by four invariant acidic residues, DEDD) and the substrate (ssDNA) binding site.
  • Structure:1CLQ_A; Enterobacteria phage RB69 family-B DNA polymerase exonuclease domain binds two calcium ions and the 3 'end of primer DNA; defined at 3.5A contacts.
    View structure with Cn3D
  • Citation:PMID 9888810

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:

Feature 1                 ####                                                                ##      
1S5J_A            192 RVAIDIEVY.[15].PIISIALAG.[ 1].DGLKKVLVL.[20].NTEYELLGRFFDILLE     YPIVLTFNG.[1]. 280  Sulfolobus sol...
1QHT_A            137 MLAFAIATL.[10].PILMISYAD      GSEARVITW.[11].STEKEMIKRFLRVVRE.[2].PDVLITYNG.[1]. 212  Thermococcus sp.
1CLQ_A            110 VANFDIEVT.[13].PIDAITHYD.[ 2].DDRFYVFDL.[40].DNEKELLMEYLNFWQQ.[2].PVILTGWNV.[1]. 219  Enterobacteria...
REF_jgi:Mlg_1353    3 VLVFDIETV.[19].EVAEAMMAL.[ 4].AGTDFQRLH.[27].DDEAELIRRFFDGVER.[1].APRLVSWNG.[1]. 106  Alkalilimnicol...
P33609            543 VMSFSMKTM.[ 8].EIIAMAALV.[ 4].ALDKAPPEP.[35].ATERTLIGFFLAKVHK.[2].PDILVGHNI.[1]. 644  house mouse
NP_001087694      317 VLSFDIECA.[12].PVIQIANMV.[ 2].QGEKDPFIR.[19].EREDALLKAWAEFVRI.[2].PDIITGYNI.[1]. 404  African clawed...
ZP_00592424       179 RMQLDIETY.[16].QVIIVSLSD.[ 1].RGWEKVIHA.[ 2].RTEKELLIELIAIIRE.[2].PDVIEGHNI.[1]. 252  Prosthecochlor...
Q07864            271 VLAFDIETT.[12].QIMMISYMI.[ 2].QGYLITNRE.[26].PDEAHLIQRWFEHVQE.[2].PTIMVTYNG.[1]. 365  human
O60673           2307 RTRRDLEPD.[ 4].PICALFYCI.[14].TGVIVIDKD.[28].ADEKALFHEIANIIKR.[2].PDILLGYEI.[1]. 2407 human
NP_615844         194 YLAFDIECL.[12].PIIMISFSF.[ 4].KGHKTLILL.[14].MDETEMLNKFFEIICE.[2].PDIVAGYNH.[1]. 278  Methanosarcina...

Feature 1             ###                                                    ##                   
1S5J_A            281 DFDLPYIYFRALKLG.[ 6].PIDVA.[ 2].DEAKYLAGLHIDLYKFF.[17].NLDAVAKALL.[3].KVKVDT 361  Sulfolobus solfata...
1QHT_A            213 NFDFAYLKKRCEELG.[10].EPKIQ.[ 5].FAVEVKGRIHFDLYPVI.[ 9].TLEAVYEAVF.[3].KEKVYA 292  Thermococcus sp.
1CLQ_A            220 SFDIPYVYNRIKNIF.[12].KTRVK.[ 9].EIITLFGISVLDYIDLY.[11].SLDYISEFEL.[3].KLKYDG 307  Enterobacteria pha...
REF_jgi:Mlg_1353  107 GFDLPVLHYRALLHG.[ 5].YWDSG.[12].NRFHDRHTDLMDVLAGY.[ 6].PLDEIATLLG.[3].KMGMSG 185  Alkalilimnicola eh...
P33609            645 SFELEVLLQRINECK.[ 9].LRRSN.[11].ERNATCGRMICDVEISA.[ 9].HLSELVQQIL.[2].ERIVIP 728  house mouse
NP_001087694      405 NFDMPYLINRAQTLK.[ 6].LGRIR.[21].KVINTEGRVQFDLLQVL.[ 9].TLNAVSFHFL.[3].KEDVQH 496  African clawed frog
ZP_00592424       253 RFDLPYLHRRCEING.[ 5].GRDQS.[18].TFYDIAGRHVIDTWFLV.[13].GLKAAAKFFG.[5].RVYVDY 346  Prosthecochloris a...
Q07864            366 FFDWPFVEARAAVHG.[ 3].QQEIG.[ 6].GEYKAPQCIHMDCLRWV.[11].NLKAAAKAKL.[3].PVELDP 441  human
O60673           2408 MHSWGYLLQRAAALS.[ 7].SRVPD.[19].SEINIVGRITLNLWRIM.[ 9].TFENVSFHVL.[3].FPLFTF 2498 human
NP_615844         279 DFDIPYITERVKALV.[18].YRKFG.[ 2].TRTEMKGRVVVDALPLV.[ 9].TLRAVSKELL.[3].KLDVPP 363  Methanosarcina ace...

Feature 1                         #   #         
1S5J_A            362 .[ 6].VEKLIEYNFRDAEITLQLTT 387  Sulfolobus solfataricus
1QHT_A            293 .[12].LERVARYSMEDAKVTYELGR 324  Thermococcus sp.
1CLQ_A            308 .[ 9].HQRYISYNIIDVYRVLQIDA 336  Enterobacteria phage RB69
REF_jgi:Mlg_1353  186 .[11].LGAVRDYCETDVLNTYLVWL 216  Alkalilimnicola ehrlichei MLHE-1
P33609            729 .[13].LLYLLEHIWKDARFILQIMC 761  house mouse
NP_001087694      497 .[13].RRRLAVYCLKDAYLPLRLLE 529  African clawed frog
ZP_00592424       347 .[10].PEKLLEYALDDVRETREIAS 376  Prosthecochloris aestuarii DSM 271
Q07864            442 .[10].PQTLATYSVSDAVATYYLYM 471  human
O60673           2499 .[14].RWKMVDHYVSRVRGNLQMLE 2532 human
NP_615844         364 .[13].FRKFVDYARRDSELALELVL 396  Methanosarcina acetivorans C2A

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