5MMS

Human cystathionine beta-synthase (CBS) p.P49L delta409-551 variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A Clinically Relevant Variant of the Human Hydrogen Sulfide-Synthesizing Enzyme Cystathionine beta-Synthase: Increased CO Reactivity as a Novel Molecular Mechanism of Pathogenicity?

Vicente, J.B.Colaco, H.G.Malagrino, F.Santo, P.E.Gutierres, A.Bandeiras, T.M.Leandro, P.Brito, J.A.Giuffre, A.

(2017) Oxid Med Cell Longev 2017: 8940321-8940321

  • DOI: https://doi.org/10.1155/2017/8940321
  • Primary Citation of Related Structures:  
    5MMS

  • PubMed Abstract: 

    The human disease classical homocystinuria results from mutations in the gene encoding the pyridoxal 5'-phosphate- (PLP-) dependent cystathionine β -synthase (CBS), a key enzyme in the transsulfuration pathway that controls homocysteine levels, and is a major source of the signaling molecule hydrogen sulfide (H 2 S). CBS activity, contributing to cellular redox homeostasis, is positively regulated by S-adenosyl-L-methionine (AdoMet) but fully inhibited upon CO or NO• binding to a noncatalytic heme moiety. Despite extensive studies, the molecular basis of several pathogenic CBS mutations is not yet fully understood. Here we found that the ferrous heme of the reportedly mild p.P49L CBS variant has altered spectral properties and markedly increased affinity for CO, making the protein much more prone than wild type (WT) CBS to inactivation at physiological CO levels. The higher CO affinity could result from the slightly higher flexibility in the heme surroundings revealed by solving at 2.80-Å resolution the crystallographic structure of a truncated p.P49L. Additionally, we report that p.P49L displays impaired H 2 S-generating activity, fully rescued by PLP supplementation along the purification, despite a minor responsiveness to AdoMet. Altogether, the results highlight how increased propensity to CO inactivation of an otherwise WT-like variant may represent a novel pathogenic mechanism in classical homocystinuria.


  • Organizational Affiliation

    Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cystathionine beta-synthase
A, B, C, D, E
A, B, C, D, E, F
408Homo sapiensMutation(s): 1 
Gene Names: CBS
EC: 4.2.1.22
UniProt & NIH Common Fund Data Resources
Find proteins for P35520 (Homo sapiens)
Explore P35520 
Go to UniProtKB:  P35520
PHAROS:  P35520
GTEx:  ENSG00000160200 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35520
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
M [auth D]
P [auth E]
G [auth A],
I [auth B],
K [auth C],
M [auth D],
P [auth E],
T [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PLP
Query on PLP

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth C]
N [auth D]
Q [auth E]
H [auth A],
J [auth B],
L [auth C],
N [auth D],
Q [auth E],
U [auth F]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
O [auth E],
R [auth E],
S [auth F]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.174α = 102.67
b = 86.783β = 103.07
c = 97.786γ = 111.19
Software Package:
Software NamePurpose
autoPROCdata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugalPTDC/SAU-MIC/111447/2009
Fundacao para a Ciencia e a TecnologiaPortugalSFRH/BPD/79224/2011
Fundacao para a Ciencia e a TecnologiaPortugalPD/BD/113990/2015
Ministero dell'Istruzione, dell'Universit? e della RicercaItalyPNR-CNR Aging Program 2012?2014
Ministero dell'Istruzione, dell'Universit? e della RicercaItalyPRIN 20158EB2CM_003
y Consiglio Nazionale delle RicercheItaly--
Federation of European Biochemical Societies--
Fundacao para a Ciencia e a Tecnologia e Ministerio da Ciencia e do Ensino SuperiorPortugaliNOVA4Health Research Unit - LISBOA-01-0145-FEDER-007344

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-08-16
    Changes: Data collection
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description