3AD7

Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with methylthio acetate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Channeling and conformational changes in the heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96.

Moriguchi, T.Ida, K.Hikima, T.Ueno, G.Yamamoto, M.Suzuki, H.

(2010) J Biochem 148: 491-505

  • DOI: https://doi.org/10.1093/jb/mvq083
  • Primary Citation of Related Structures:  
    3AD7, 3AD8, 3AD9, 3ADA

  • PubMed Abstract: 

    We characterized the crystal structures of heterotetrameric sarcosine oxidase (SO) from Corynebacterium sp. U-96 complexed with methylthioacetate (MTA), pyrrole 2-carboxylate (PCA) and sulphite, and of sarcosine-reduced SO. SO comprises α-, β-, γ- and δ-subunits; FAD and FMN cofactors; and a large internal cavity. MTA and PCA are sandwiched between the re-face of the FAD isoalloxazine ring and the β-subunit C-terminal residues. Reduction of flavin cofactors shifts the β-subunit Ala1 towards the α-subunit Met55, forming a surface cavity at the oxygen-channel vestibule and rendering the β-subunit C-terminal residues mobile. We identified three channels connecting the cavity and the enzyme surface. Two of them exist in the inter-subunit space between α and β-subunits, and the substrate sarcosine seems to enter the active site through either of these channels and reaches the re-side of the FAD isoalloxazine ring by traversing the mobile β-subunit C-terminal residues. The third channel goes through the α-subunit and has a folinic acid-binding site, where the iminium intermediate is converted to Gly and either formaldehyde or, 5,10-methylenetetrahydrofolate. Oxygen molecules are probably located on the surface cavity and diffuse to the FMN isoalloxazine ring; the H(2)O(2) formed exits via the oxygen channel.


  • Organizational Affiliation

    Division of Bioscience, Graduate School of Fundamental Life Science, Kitasato University, Kitasato 1-15-1, Sagamihara, Kanagawa 252-0329, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit alpha of sarcosine oxidase964Corynebacterium sp. U-96Mutation(s): 0 
Gene Names: soxA
UniProt
Find proteins for Q50LF0 (Corynebacterium sp. (strain U-96))
Explore Q50LF0 
Go to UniProtKB:  Q50LF0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ50LF0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit beta of sarcosine oxidase404Corynebacterium sp. U-96Mutation(s): 0 
Gene Names: soxB
EC: 1.5.3.1
UniProt
Find proteins for Q50LF2 (Corynebacterium sp. (strain U-96))
Explore Q50LF2 
Go to UniProtKB:  Q50LF2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ50LF2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit gamma of sarcosine oxidase203Corynebacterium sp. U-96Mutation(s): 0 
Gene Names: soxG
UniProt
Find proteins for Q50LE9 (Corynebacterium sp. (strain U-96))
Explore Q50LE9 
Go to UniProtKB:  Q50LE9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ50LE9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit delta of sarcosine oxidase99Corynebacterium sp. U-96Mutation(s): 0 
Gene Names: soxD
UniProt
Find proteins for Q50LF1 (Corynebacterium sp. (strain U-96))
Explore Q50LF1 
Go to UniProtKB:  Q50LF1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ50LF1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
K [auth B]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAD
Query on NAD

Download Ideal Coordinates CCD File 
E [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
FMN
Query on FMN

Download Ideal Coordinates CCD File 
L [auth B]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
MTG
Query on MTG

Download Ideal Coordinates CCD File 
M [auth B][METHYLTHIO]ACETATE
C3 H5 O2 S
HGTBAIVLETUVCG-UHFFFAOYSA-M
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],
N [auth B],
O [auth B],
P [auth C],
R [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
Q [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
MTG PDBBind:  3AD7 Kd: 3.01e+6 (nM) from 1 assay(s)
Binding MOAD:  3AD7 Kd: 3.01e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 198.949α = 90
b = 198.949β = 90
c = 196.765γ = 120
Software Package:
Software NamePurpose
SPACEdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-09-04
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description