Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: authors reported there is no experimental evidence

Macromolecule Content

• Total Structure Weight: 48710.81 
• Atom Count: 3313 
• Residue Count: 366 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

6CTU

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CFCL, beta, gamma dCTP analogue

• DOI: 10.2210/pdb6CTU/pdb
• NDB: 6CTU

• Classification: transcription/dna
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2018-03-23 Released: 2018-06-20 
• Deposition Author(s): Batra, V.K., Wilson, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.206 
• R-Value Work: 0.171 

Literature

Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.

Batra, V.K., Oertell, K., Beard, W.A., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Wilson, S.H.

(2018) Biochemistry 57: 3934-3944

• PubMed: 29874056 
• DOI: 10.1021/acs.biochem.8b00418
• Primary Citation of Related Structures:  
  6BEM, 6BEL, 6CR6, 6G2Q, 6CTX, 6CTW, 6CTV, 6CTT, 6CTR, 6CTQ, 6CTP, 6CTO, 6CTN, 6CTM, 6CTL, 6CTK, 6CTJ, 6CTI, 6CRC, 6CRB, 6CR9, 6CR8, 6CR7, 6CR5, 6CR4, 6CR3


• PubMed Abstract: 
  

We report high-resolution crystal structures of DNA polymerase (pol) β in ternary complex with a panel of incoming dNTPs carrying acidity-modified 5'-triphosphate groups. These novel dNTP analogues have a variety of halomethylene substitutions replacing the bridging oxygen between Pβ and Pγ of the incoming dNTP, whereas other analogues have alkaline substitutions at the bridging oxygen. Use of these analogues allows the first systematic comparison of effects of 5'-triphosphate acidity modification on active site structures and the rate constant of DNA synthesis. These ternary complex structures with incoming dATP, TTP and dCTP analogues reveal the enzyme's active site is not grossly altered by the acidity modifications of the triphosphate group. Yet, with analogues of all three incoming dNTP bases, subtle structural differences are apparent in interactions around the nascent base pair and at the guanidinium groups of active site arginine residues. These results are important in understanding how acidity modification of the incoming dNTP's 5'-triphosphate can influence DNA polymerase activity and the significance of interactions at arginines 183 and 149 in the active site.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
DNA polymerase beta	A	335	Homo sapiens	Mutation(s): 0  Gene Names: POLB EC: 2.7.7.7, 4.2.99.-
Find proteins for P06746 (Homo sapiens) Go to Gene View: POLB Go to UniProtKB:  P06746

Entity ID: 1
Molecule	Chains	Length	Organism
DNA (5'-D(*CP*CP*GP*AP*CP*GP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')	T	16	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(2DA))-3')	P	10	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism
DNA (5'-D(P*GP*TP*CP*GP*G)-3')	D	5	Homo sapiens

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
DC	A	2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE C9 H14 N3 O7 P NCMVOABPESMRCP-SHYZEUOFSA-N
VC6	A	4-amino-1-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one C10 H16 Cl F N3 O12 P3 KEKPFSDJAHISFV-VBOXYBSHSA-N
NA	A, D, P	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	A, T	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2DA	P	DNA LINKING	C10 H14 N5 O5 P		DA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.206 
• R-Value Work: 0.171 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 50.810	α = 90.00
b = 79.636	β = 107.78
c = 55.483	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	phasing
HKL-2000	data reduction
PDB_EXTRACT	data extraction
PHENIX	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-03-23 
• Released Date: 2018-06-20 
• Deposition Author(s): Batra, V.K., Wilson, S.H.

Revision History 

• Version 1.0: 2018-06-20
  Type: Initial release
• Version 1.1: 2018-07-11
  Type: Data collection, Database references