Structure of PDB 3rma Chain A

Receptor sequence

>3rmaA (length=894) Species: 12353 (Escherichia phage RB69)

MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYF
DIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYE
IKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFD
LLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRV
KEIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPI
SKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF
SPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMS
FDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPN
GMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS
VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINR
KLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVC
GTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERM
EPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYA
LNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEES
LQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGIL
TYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIK
DDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFDF

3D structure

• PDB: 3rma A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complex.
• Chain: A
• Resolution: 2.84 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.
  3.1.11.-

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	P392 G393 A394 K705 R707 P799 K800 C801 K874	P383 G384 A385 K696 R698 P790 K791 C792 K865
BS02	dna	A	T622 M728 Q733 K734 S735 S784 N786 K790 Y791 H804	T613 M719 Q724 K725 S726 S775 N777 K781 Y782 H795
BS03	dna	A	S36 F38 Y49 R59 M85 D95 F370 K374 K378 V379 I380	S36 F38 Y49 R59 M85 D95 F361 K365 K369 V370 I371

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0004527 exonuclease activity
• GO:0008408 3'-5' exonuclease activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication
• GO:0039686 bidirectional double-stranded viral DNA replication
• GO:0039693 viral DNA genome replication

External links

• PDB: RCSB:3rma, PDBe:3rma, PDBj:3rma
• PDBsum: 3rma
• PubMed: 21781974
• UniProt: Q38087|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)