1CKN | pdb_00001ckn

STRUCTURE OF GUANYLYLATED MRNA CAPPING ENZYME COMPLEXED WITH GTP

PDB DOI: https://doi.org/10.2210/pdb1CKN/pdb

Classification: CAPPING ENZYME
Organism(s): Paramecium bursaria Chlorella virus 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1997-04-20 Released: 1997-07-07
Deposition Author(s): Hakansson, K., Doherty, A.J., Wigley, D.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.299 (Depositor)
R-Value Work:
0.224 (Depositor), 0.206 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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Literature

X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes.

Hakansson, K., Doherty, A.J., Shuman, S., Wigley, D.B.

(1997) Cell 89: 545-553

PubMed: 9160746 Search on PubMed
DOI: https://doi.org/10.1016/s0092-8674(00)80236-6
Primary Citation Related Structures:
1CKM, 1CKN

PubMed Abstract:
We have solved the crystal structure of an mRNA capping enzyme at 2.5 A resolution. The enzyme comprises two domains with a deep, but narrow, cleft between them. The two molecules in the crystallographic asymmetric unit adopt very different conformations; both contain a bound GTP, but one protein molecule is in an open conformation while the other is in a closed conformation. Only in the closed conformation is the enzyme able to bind manganese ions and undergo catalysis within the crystals to yield the covalent guanylated enzyme intermediate. These structures provide direct evidence for a mechanism that involves a significant conformational change in the enzyme during catalysis.

Organizational Affiliation

Laboratory of Molecular Biophysics, University of Oxford, United Kingdom.

Macromolecule Content

Total Structure Weight: 76.79 kDa
Atom Count: 5,525
Modeled Residue Count: 634
Deposited Residue Count: 660
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MRNA CAPPING ENZYME	A	330	Paramecium bursaria Chlorella virus 1	Mutation(s): 0 EC: 2.7.7.50
UniProt
Find proteins for Q84424 (Paramecium bursaria Chlorella virus 1) Explore Q84424 Go to UniProtKB: Q84424
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q84424
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MRNA CAPPING ENZYME	B	330	Paramecium bursaria Chlorella virus 1	Mutation(s): 0 EC: 2.7.7.50
UniProt
Find proteins for Q84424 (Paramecium bursaria Chlorella virus 1) Explore Q84424 Go to UniProtKB: Q84424
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q84424
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
GPL Query on GPL	B	L-PEPTIDE LINKING	C₁₆ H₂₆ N₇ O₉ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.299 (Depositor)
R-Value Work: 0.224 (Depositor), 0.206 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.906	α = 90
b = 212.953	β = 90
c = 105.016	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 1997-07-07

Deposition Author(s):

Hakansson, K.

Doherty, A.J.

Wigley, D.B.

Revision History (Full details and data files)

Version 1.0: 1997-07-07
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-09
Changes: Database references, Derived calculations, Other, Refinement description