9JFF | pdb_00009jff

Crystal structure of L-threonine-O-3-phosphate decarboxylase CobC in complex with reaction intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.192 (Depositor), 0.193 (DCC) 
  • R-Value Work: 
    0.156 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
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Literature

Crystal structure of l-threonine-O-3-phosphate decarboxylase CobC from Sinorhizobium meliloti involved in vitamin B 12 biosynthesis.

Jiang, M.Guo, S.Chen, X.Wei, Q.Wang, M.

(2024) Biochem Biophys Res Commun 734: 150767-150767

  • DOI: https://doi.org/10.1016/j.bbrc.2024.150767
  • Primary Citation Related Structures: 
    9JFB, 9JFF

  • PubMed Abstract: 

    Vitamin B 12 is involved in many important biochemical reactions for humans, and its deficiency can lead to serious diseases. The industrial production of vitamin B 12 is achieved through microbial fermentation. In this work, we determine the crystal structures of the l-threonine-O-3-phosphate (Thr-P) decarboxylase CobC from Sinorhizobium meliloti (SmCobC), an industrial vitamin B 12 -producing bacterium, in apo form and in complex with a reaction intermediate. Our structures supported the Thr-P decarboxylase activity of SmCobC and revealed that the positively charged substrate-binding pocket between the large and small domains determines its substrate selectivity for Thr-P. Moreover, our results provided evidence for the proposition that the AP-P linker is formed by direct incorporation of AP-P in the biosynthetic pathway of vitamin B 12 in S.meliloti.


  • Organizational Affiliation
    • Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China; School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China.

Macromolecule Content 

  • Total Structure Weight: 37.68 kDa 
  • Atom Count: 3,097 
  • Modeled Residue Count: 333 
  • Deposited Residue Count: 341 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
threonine-phosphate decarboxylase341Sinorhizobium melilotiMutation(s): 0 
Gene Names: cobC
EC: 4.1.1.81
UniProt
Find proteins for A0A499W357 (Rhizobium meliloti)
Explore A0A499W357 
Go to UniProtKB:  A0A499W357
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A499W357
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
33P
(Subject of Investigation/LOI)

Query on 33P



Download:Ideal Coordinates CCD File
E [auth A]{3-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-PROPYL}-PHOSPHONIC ACID
C11 H20 N2 O9 P2
JMZWWHLIKAYMPJ-SSDOTTSWSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
N [auth A],
O [auth A],
P [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
Q [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.192 (Depositor), 0.193 (DCC) 
  • R-Value Work:  0.156 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.074α = 90
b = 160.074β = 90
c = 160.074γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChina2108085MC75

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release