6OUX | pdb_00006oux

Structure of SMUL_1544, a decarboxylase from Sulfurospirillum multivorans

• PDB DOI: https://doi.org/10.2210/pdb6OUX/pdb

• Classification: LYASE
• Organism(s): Sulfurospirillum multivorans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-05 Released: 2019-06-05 
• Deposition Author(s): Wetterhorn, K.M., Rayment, I., Vecellio, A., Seeger, M., Keller, S., Schubert, T.
• Funding Organization(s): National Institutes of Health/National Library of Medicine (NIH/NLM)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.250 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Structural and functional analysis of an l-serine O-phosphate decarboxylase involved in norcobamide biosynthesis.

Keller, S., Wetterhorn, K.M., Vecellio, A., Seeger, M., Rayment, I., Schubert, T.

(2019) FEBS Lett 593: 3040-3053

• PubMed: 31325159 
• DOI: https://doi.org/10.1002/1873-3468.13543
• Primary Citation Related Structures: 
  6OUX


• PubMed Abstract: 
  

  Structural diversity of natural cobamides (Cbas, B ₁₂ vitamers) is limited to the nucleotide loop. The loop is connected to the cobalt-containing corrin ring via an (R)-1-aminopropan-2-ol O-2-phosphate (AP-P) linker moiety. AP-P is produced by the l-threonine O-3-phosphate (l-Thr-P) decarboxylase CobD. Here, the CobD homolog SMUL_1544 of the organohalide-respiring epsilonproteobacterium Sulfurospirillum multivorans was characterized as a decarboxylase that produces ethanolamine O-phosphate (EA-P) from l-serine O-phosphate (l-Ser-P). EA-P is assumed to serve as precursor of the linker moiety of norcobamides that function as cofactors in the respiratory reductive dehalogenase. SMUL_1544 (SmCobD) is a pyridoxal-5'-phosphate (PLP)-containing enzyme. The structural analysis of the SmCobD apoprotein combined with the characterization of truncated mutant proteins uncovered a role of the SmCobD N-terminus in efficient l-Ser-P conversion.

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Organizational Affiliation: 
• Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, WI, USA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 90.24 kDa 
• Atom Count: 6,528 
• Modeled Residue Count: 747 
• Deposited Residue Count: 786 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Threonine phosphate decarboxylase-like enzyme	A, B	393	Sulfurospirillum multivorans	Mutation(s): 0  Gene Names: SMUL_1544 EC: 4.1.1
UniProt
Find proteins for P0DV65 (Sulfurospirillum multivorans (strain DM 12446 / JCM 15788 / NBRC 109480)) Explore P0DV65  Go to UniProtKB:  P0DV65

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.250 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.53	α = 90
b = 90.627	β = 109.96
c = 70.867	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-06-05 
Deposition Author(s): Wetterhorn, K.M., Rayment, I., Vecellio, A., Seeger, M., Keller, S., Schubert, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Library of Medicine (NIH/NLM)	United States	--

Revision History  

• Version 1.0: 2019-06-05
  Type: Initial release
  
• Version 1.1: 2019-07-31
  Changes: Data collection, Database references
• Version 1.2: 2019-11-20
  Changes: Database references
• Version 1.3: 2019-12-18
  Changes: Author supporting evidence
• Version 1.4: 2023-10-11
  Changes: Data collection, Database references, Refinement description