6HZ5

Structure of McrBC without DNA binding domains (Class 1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-based mechanism for activation of the AAA+ GTPase McrB by the endonuclease McrC.

Nirwan, N.Itoh, Y.Singh, P.Bandyopadhyay, S.Vinothkumar, K.R.Amunts, A.Saikrishnan, K.

(2019) Nat Commun 10: 3058-3058

  • DOI: 10.1038/s41467-019-11084-1
  • Primary Citation of Related Structures:  
    6HZ4, 6HZ5, 6HZ6, 6HZ7, 6HZ8, 6HZ9

  • PubMed Abstract: 
  • The AAA+ GTPase McrB powers DNA cleavage by the endonuclease McrC. The GTPase itself is activated by McrC. The architecture of the GTPase and nuclease complex, and the mechanism of their activation remained unknown. Here, we report a 3.6 Å structure of a GTPase-active and DNA-binding deficient construct of McrBC ...

    The AAA+ GTPase McrB powers DNA cleavage by the endonuclease McrC. The GTPase itself is activated by McrC. The architecture of the GTPase and nuclease complex, and the mechanism of their activation remained unknown. Here, we report a 3.6 Å structure of a GTPase-active and DNA-binding deficient construct of McrBC. Two hexameric rings of McrB are bridged by McrC dimer. McrC interacts asymmetrically with McrB protomers and inserts a stalk into the pore of the ring, reminiscent of the γ subunit complexed to α 3 β 3 of F 1 -ATPase. Activation of the GTPase involves conformational changes of residues essential for hydrolysis. Three consecutive nucleotide-binding pockets are occupied by the GTP analogue 5'-guanylyl imidodiphosphate and the next three by GDP, which is suggestive of sequential GTP hydrolysis.


    Organizational Affiliation

    Division of Biology, Indian Institute of Science Education and Research, Pune, 411008, India. saikrishnan@iiserpune.ac.in.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5-methylcytosine-specific restriction enzyme B
A,
B,
C,
D,
E,
307Escherichia coli K-12Mutation(s): 0 
Gene Names: mcrBrglBb4346JW5871
EC: 3.1.21
UniProt
Find proteins for P15005 (Escherichia coli (strain K12))
Explore P15005 
Go to UniProtKB:  P15005
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15005
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein McrCG [auth M],
N
348Escherichia coli K-12Mutation(s): 0 
Gene Names: mcrCb4345JW5789
UniProt
Find proteins for P15006 (Escherichia coli (strain K12))
Explore P15006 
Go to UniProtKB:  P15006
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15006
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP (Subject of Investigation/LOI)
Query on GNP

Download Ideal Coordinates CCD File 
BA [auth I],
O [auth A],
Q [auth B],
S [auth C],
X [auth G],
BA [auth I],
O [auth A],
Q [auth B],
S [auth C],
X [auth G],
Z [auth H]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
DA [auth J],
EA [auth K],
FA [auth L],
U [auth D],
V [auth E],
DA [auth J],
EA [auth K],
FA [auth L],
U [auth D],
V [auth E],
W [auth F]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth H],
CA [auth I],
P [auth A],
R [auth B],
T [auth C],
AA [auth H],
CA [auth I],
P [auth A],
R [auth B],
T [auth C],
Y [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Refinement description