1VE3 | pdb_00001ve3

Crystal structure of PH0226 protein from Pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb1VE3/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-03-26 Released: 2005-05-24 
• Deposition Author(s): Lokanath, N.K., Yamamoto, H., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.270 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Literature

Crystal structure of SAM-dependent methyltransferase from Pyrococcus horikoshii.

Pampa, K.J., Madan Kumar, S., Hema, M.K., Kumara, K., Naveen, S., Kunishima, N., Lokanath, N.K.

(2017) Acta Crystallogr F Struct Biol Commun 73: 706-712

• PubMed: 29199993 
• DOI: https://doi.org/10.1107/S2053230X17016648
• Primary Citation Related Structures: 
  1VE3


• PubMed Abstract: 
  

  Methyltransferases (MTs) are enzymes involved in methylation that are needed to perform cellular processes such as biosynthesis, metabolism, gene expression, protein trafficking and signal transduction. The cofactor S-adenosyl-L-methionine (SAM) is used for catalysis by SAM-dependent methyltransferases (SAM-MTs). The crystal structure of Pyrococcus horikoshii SAM-MT was determined to a resolution of 2.1 Å using X-ray diffraction. The monomeric structure consists of a Rossmann-like fold (domain I) and a substrate-binding domain (domain II). The cofactor (SAM) molecule binds at the interface between adjacent subunits, presumably near to the active site(s) of the enzyme. The observed dimeric state might be important for the catalytic function of the enzyme.

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Organizational Affiliation: 
• Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru, Karnataka 570 006, India.
PURSE Laboratory, Mangalore University, Mangalagangotri, Mangalore, Karnataka 574 199, India.
Department of Studies in Physics, University of Mysore, Manasagangotri, Mysuru, Karnataka 570 006, India.
Institution of Excellence, University of Mysore, Manasagangotri, Mysuru, Karnataka 570 006, India.
Advanced Protein Crystallography Research Group, RIKEN Spring-8 Center, Harima Institute, 1-1-1 Koyto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 54.92 kDa 
• Atom Count: 3,887 
• Modeled Residue Count: 438 
• Deposited Residue Count: 454 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein PH0226	A, B	227	Pyrococcus horikoshii	Mutation(s): 0
UniProt
Find proteins for O57965 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57965  Go to UniProtKB:  O57965

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A], D [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.270 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.167	α = 90
b = 58.167	β = 90
c = 252.463	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-24 
Deposition Author(s): Lokanath, N.K., Yamamoto, H., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-05-24
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-12-13
  Changes: Database references
• Version 1.4: 2020-01-01
  Changes: Database references, Derived calculations
• Version 1.5: 2020-01-22
  Changes: Derived calculations
• Version 1.6: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.7: 2024-10-30
  Changes: Structure summary