SCOPe 2.08: Domain d2oyqd1: 2oyq D:2-375

Lineage for d2oyqd1 (2oyq D:2-375)

1. Root: SCOPe 2.08

2. Class c: Alpha and beta proteins (a/b) [51349] (148 folds)

3. Fold c.55: Ribonuclease H-like motif [53066] (7 superfamilies)
   3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest

4. Superfamily c.55.3: Ribonuclease H-like [53098] (18 families)
   consists of one domain of this fold

5. Family c.55.3.5: DnaQ-like 3'-5' exonuclease [53118] (17 proteins)
   contains Pfam PF00929

6. Protein Exonuclease domain of family B DNA polymerases [53125] (8 species)
   elaborated with additional structures and the N-terminal subdomain

7. Species Bacteriophage RB69 [TaxId:12353] [53127] (93 PDB entries)
   additional N-terminal subdomain contains rudimental OB-fold and rudimental ferredoxin-like fold

8. Domain d2oyqd1: 2oyq D:2-375 [149076]
   Other proteins in same PDB: d2oyqa2, d2oyqb2, d2oyqc2, d2oyqd2
   automated match to d1ig9a1
   protein/DNA complex; complexed with mg, n5p
   has additional subdomain(s) that are not in the common domain

Details for d2oyqd1

PDB Entry: 2oyq, 2.86 Å

PDB Description: crystal structure of rb69 gp43 in complex with dna with 5-nimp opposite an abasic site analog

PDB Compounds: (D:) DNA polymerase

SCOPe Domain Sequences for d2oyqd1:

Sequence, based on SEQRES records:

>d2oyqd1 c.55.3.5 (D:2-375) Exonuclease domain of family B DNA polymerases {Bacteriophage RB69 [TaxId: 12353]}
kefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrkl
fanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtspd
gfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevpse
iidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestakr
lsphrktrvkvienmygsreiitlfgisvldyidlykkfsftnqpsysldyisefelnvg
klkydgpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfsp
iktwdaiifnslke

Sequence, based on observed residues (ATOM records):

>d2oyqd1 c.55.3.5 (D:2-375) Exonuclease domain of family B DNA polymerases {Bacteriophage RB69 [TaxId: 12353]}
kefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrkl
fanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtspd
gfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaggdevpseiidki
iympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestakrlsphr
ktrvkvienmygsreiitlfgisvldyidlykkfsftnqpsysldyisefelnvgklkyd
gpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfspiktwd
aiifnslke

Timeline for d2oyqd1:

• d2oyqd1 first appeared in SCOP 1.75
  
• d2oyqd1 appears in SCOPe 2.07