Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 84.45 kDa 
• Atom Count: 5748 
• Residue Count: 744 
• Unique protein chains: 1

1F38

X-RAY CRYSTALLOGRAPHIC STRUCTURE OF PRECORRIN 8W DECARBOXYLASE, THE PRODUCT OF GENE MT0146 IN THE METHANOBACTERIUM THERMOAUTOTROPHICUM GENOME

• DOI: 10.2210/pdb1F38/pdb

• Classification: LYASE
• Organism(s): Methanothermobacter thermautotrophicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-05-31 Released: 2003-06-10 
• Deposition Author(s): Keller, J.P., Smith, P.M., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.291 
• R-Value Work: 0.236 

Literature

The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase is a methyltransferase

Keller, J.P., Smith, P.M., Benach, J., Christendat, D., deTitta, G.T., Hunt, J.F.

(2002) Structure 10: 1475-1487

• PubMed: 12429089 
• DOI: 10.1016/s0969-2126(02)00876-6
• Primary Citation of Related Structures:  
  1F38, 1L3I, 1L3C, 1L3B, 1KXZ


• PubMed Abstract: 
  

The CbiT and CbiE enzymes participate in the biosynthesis of vitamin B12. They are fused together in some organisms to form a protein called CobL, which catalyzes two methylations and one decarboxylation on a precorrin intermediate. Because CbiE has sequence homology to canonical precorrin methyltransferases, CbiT was hypothesized to catalyze the decarboxylation. We herein present the crystal structure of MT0146, the CbiT homolog from Methanobacterium thermoautotrophicum. The protein shows structural similarity to Rossmann-like S-adenosyl-methionine-dependent methyltransferases, and our 1.9 A cocrystal structure shows that it binds S-adenosyl-methionine in standard geometry near a binding pocket that could accommodate a precorrin substrate. Therefore, MT0146/CbiT probably functions as a precorrin methyltransferase and represents the first enzyme identified with this activity that does not have the canonical precorrin methyltransferase fold.

---

Organizational Affiliation: 

Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PRECORRIN-8W DECARBOXYLASE	A, B, C, D	192	Methanothermobacter thermautotrophicus	Mutation(s): 8  Gene Names: MT0146 EC: 2.1.1.196
Find proteins for O26249 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26249  Go to UniProtKB:  O26249

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.291 
• R-Value Work: 0.236 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.47	α = 90
b = 194.76	β = 90
c = 59.24	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-05-31 
• Released Date: 2003-06-10 
Deposition Author(s): Keller, J.P., Smith, P.M., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History 

• Version 1.0: 2003-06-10
  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: 2018-01-31
  Changes: Experimental preparation