1X31

Crystal Structure of Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96

PDB DOI: https://doi.org/10.2210/pdb1X31/pdb

Classification: OXIDOREDUCTASE
Organism(s): Corynebacterium sp. U-96
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-04-27 Released: 2005-07-05
Deposition Author(s): Ida, K., Moriguchi, T., Suzuki, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.232
R-Value Work: 0.188
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96

Ida, K., Moriguchi, T., Suzuki, H.

(2005) Biochem Biophys Res Commun 333: 359-366

PubMed: 15946648 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2005.05.116
Primary Citation of Related Structures:
1VRQ, 1X31

PubMed Abstract:
Sarcosine oxidase from Corynebacterium sp. U-96 is a heterotetrameric enzyme. Here we report the crystal structures of the enzyme in complex with dimethylglycine and folinic acid. The alpha subunit is composed of two domains, contains NAD(+), and binds folinic acid. The beta subunit contains dimethylglycine, FAD, and FMN, and these flavins are approximately 10A apart. The gamma subunit is in contact with two domains of alpha subunit and has possibly a folate-binding structure. The delta subunit contains a single atom of zinc and has a Cys(3)His zinc finger structure. Based on the structures determined and on the previous works, the structure-function relationship on the heterotetrameric sarcosine oxidase is discussed.

Organizational Affiliation

Department of Biosciences, School of Science, Kitasato University, 1-15-1 Kitasato, Sagamihara, Kanagawa 228-8555, Japan. idakoh@sci.kitasato-u.ac.jp

Macromolecule Content

Total Structure Weight: 182.92 kDa
Atom Count: 13,814
Modelled Residue Count: 1,651
Deposited Residue Count: 1,673
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sarcosine oxidase alpha subunit	A	964	Corynebacterium sp. U-96	Mutation(s): 0 EC: 1.5.3.1
UniProt
Find proteins for Q50LF0 (Corynebacterium sp. (strain U-96)) Explore Q50LF0 Go to UniProtKB: Q50LF0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q50LF0
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sarcosine oxidase beta subunit	B	404	Corynebacterium sp. U-96	Mutation(s): 0 EC: 1.5.3.1
UniProt
Find proteins for Q50LF2 (Corynebacterium sp. (strain U-96)) Explore Q50LF2 Go to UniProtKB: Q50LF2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q50LF2
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Sarcosine oxidase gamma subunit	C	206	Corynebacterium sp. U-96	Mutation(s): 0 EC: 1.5.3.1
UniProt
Find proteins for Q50LE9 (Corynebacterium sp. (strain U-96)) Explore Q50LE9 Go to UniProtKB: Q50LE9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q50LE9
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Sarcosine oxidase delta subunit	D	99	Corynebacterium sp. U-96	Mutation(s): 0 EC: 1.5.3.1
UniProt
Find proteins for Q50LF1 (Corynebacterium sp. (strain U-96)) Explore Q50LF1 Go to UniProtKB: Q50LF1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q50LF1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B]	L [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B]	M [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
DMG Query on DMG Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B]	N [auth B]	N,N-DIMETHYLGLYCINE C₄ H₉ N O₂ FFDGPVCHZBVARC-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], O [auth C], Q [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain Q [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain P [auth D] MOL2 format, chain P [auth D]	P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain P [auth D] Interactions & Density Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.232
R-Value Work: 0.188
R-Value Observed: 0.188
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 199.112	α = 90
b = 199.112	β = 90
c = 197.205	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-07-05

Deposition Author(s):

Ida, K.

Moriguchi, T.

Suzuki, H.

Revision History (Full details and data files)

Version 1.0: 2005-07-05
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations