3AD8

Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with pyrrole 2-carboxylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

Starting Model: experimental
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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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SARCOSINE OXIDASE ALPHA SUBUNIT964Corynebacterium sp. U-96Mutation(s): 0 
Gene Names: soxA
EC: 1.5.3.24
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
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SARCOSINE OXIDASE BETA SUBUNIT404Corynebacterium sp. U-96Mutation(s): 0 
Gene Names: soxB
EC: 1.5.3.1 (PDB Primary Data), 1.5.3.24 (UniProt)
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
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SARCOSINE OXIDASE GAMMA SUBUNIT203Corynebacterium sp. U-96Mutation(s): 0 
Gene Names: soxG
EC: 1.5.3.24
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
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
SARCOSINE OXIDASE DELTA SUBUNIT99Corynebacterium sp. U-96Mutation(s): 0 
Gene Names: soxD
EC: 1.5.3.24
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
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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

Download Ideal Coordinates CCD File 
O [auth B]PYRROLE-2-CARBOXYLATE
C5 H4 N O2
WRHZVMBBRYBTKZ-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],
K [auth A],
L [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth C],
U [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
T [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
PYC PDBBind:  3AD8 Kd: 6.90e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 198.796α = 90
b = 198.796β = 90
c = 196.819γ = 120
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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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