SCOPe 2.06: Domain d4khya1: 4khy A:1-375

Lineage for d4khya1 (4khy A:1-375)

1. Root: SCOPe 2.06

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] (15 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] (92 PDB entries)
   additional N-terminal subdomain contains rudimental OB-fold and rudimental ferredoxin-like fold

8. Domain d4khya1: 4khy A:1-375 [235167]
   Other proteins in same PDB: d4khya2
   automated match to d4khqa1
   protein/DNA complex; complexed with ca, na, ttp; mutant

Details for d4khya1

PDB Entry: 4khy, 2.25 Å

PDB Description: Ternary complex of rb69 mutant L415F with ribonucleotide at -3 position

PDB Compounds: (A:) DNA polymerase

SCOPe Domain Sequences for d4khya1:

Sequence, based on SEQRES records:

>d4khya1 c.55.3.5 (A:1-375) Exonuclease domain of family B DNA polymerases {Bacteriophage RB69 [TaxId: 12353]}
mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
rlsphrktrvkvienmygsreiitlfgisvldyidlykkfsftnqpsysldyisefelnv
gklkydgpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfs
piktwdaiifnslke

Sequence, based on observed residues (ATOM records):

>d4khya1 c.55.3.5 (A:1-375) Exonuclease domain of family B DNA polymerases {Bacteriophage RB69 [TaxId: 12353]}
mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
rlsphrktrvkviensreiitlfgisvldyidlykkfsftnqpsysldyisefelnvgkl
kydgpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfspik
twdaiifnslke

Timeline for d4khya1:

• d4khya1 first appeared in SCOPe 2.03
  
• d4khya1 appears in SCOPe 2.05
  
• d4khya1 appears in SCOPe 2.07
  
• d4khya1 appears in the current release, SCOPe 2.08