1OH7 | pdb_00001oh7

THE CRYSTAL STRUCTURE OF E. COLI MUTS BINDING TO DNA WITH A G:G MISMATCH

• PDB DOI: https://doi.org/10.2210/pdb1OH7/pdb
• NAKB: 1OH7

• Classification: DNA BINDING
• Organism(s): Escherichia coli, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-05-23 Released: 2003-08-08 
• Deposition Author(s): Natrajan, G., Lamers, M.H., Enzlin, J.H., Winterwerp, H.H.K., Perrakis, A., Sixma, T.K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Structures of E. Coli DNA Mismatch Repair Enzyme Muts in Complex with Different Mismatches: A Common Recognition Mode for Diverse Substrates

Natrajan, G., Lamers, M.H., Enzlin, J.H., Winterwerp, H.H.K., Perrakis, A., Sixma, T.K.

(2003) Nucleic Acids Res 31: 4814

• PubMed: 12907723 
• DOI: https://doi.org/10.1093/nar/gkg677
• Primary Citation Related Structures: 
  1OH5, 1OH6, 1OH7, 1OH8


• PubMed Abstract: 
  

  We have refined a series of isomorphous crystal structures of the Escherichia coli DNA mismatch repair enzyme MutS in complex with G:T, A:A, C:A and G:G mismatches and also with a single unpaired thymidine. In all these structures, the DNA is kinked by approximately 60 degrees upon protein binding. Two residues widely conserved in the MutS family are involved in mismatch recognition. The phenylalanine, Phe 36, is seen stacking on one of the mismatched bases. The same base is also seen forming a hydrogen bond to the glutamate Glu 38. This hydrogen bond involves the N7 if the base stacking on Phe 36 is a purine and the N3 if it is a pyrimidine (thymine). Thus, MutS uses a common binding mode to recognize a wide range of mismatches.

---

Organizational Affiliation: 
• Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 198.15 kDa 
• Atom Count: 13,004 
• Modeled Residue Count: 1,577 
• Deposited Residue Count: 1,660 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA MISMATCH REPAIR PROTEIN MUTS	A, B	800	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P23909 (Escherichia coli (strain K12)) Explore P23909  Go to UniProtKB:  P23909

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP *CP*AP*CP*CP*AP*GP*TP*GP*TP*CP*AP*GP*CP*GP*TP *CP*CP*TP*AP*T)-3'	C [auth E]	30	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*AP*TP*AP*GP*GP*AP*CP*GP*CP*TP *GP*AP*CP*AP*CP*TP*GP*GP*TP*GP*CP*GP*TP*GP*GP *CP*AP*GP*CP*T)-3'	D [auth F]	30	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.413	α = 90
b = 91.81	β = 90
c = 260.444	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-08-08 
Deposition Author(s): Natrajan, G., Lamers, M.H., Enzlin, J.H., Winterwerp, H.H.K., Perrakis, A., Sixma, T.K.

Revision History  

• Version 1.0: 2003-08-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2020-07-29
  Changes: Derived calculations, Other, Source and taxonomy
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Refinement description