6C2Q

Crystal Structures of Cystathionine beta-Synthase from Saccharomyces cerevisiae: the Structure of the PLP-L-Serine Intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Crystal Structures of Cystathionine beta-Synthase from Saccharomyces cerevisiae: One Enzymatic Step at a Time.

Tu, Y.Kreinbring, C.A.Hill, M.Liu, C.Petsko, G.A.McCune, C.D.Berkowitz, D.B.Liu, D.Ringe, D.

(2018) Biochemistry 57: 3134-3145

  • DOI: https://doi.org/10.1021/acs.biochem.8b00092
  • Primary Citation of Related Structures:  
    6C2H, 6C2Q, 6C2Z, 6C4P

  • PubMed Abstract: 

    Cystathionine β-synthase (CBS) is a key regulator of sulfur amino acid metabolism, taking homocysteine from the methionine cycle to the biosynthesis of cysteine via the trans-sulfuration pathway. CBS is also a predominant source of H 2 S biogenesis. Roles for CBS have been reported for neuronal death pursuant to cerebral ischemia, promoting ovarian tumor growth, and maintaining drug-resistant phenotype by controlling redox behavior and regulating mitochondrial bioenergetics. The trans-sulfuration pathway is well-conserved in eukaryotes, but the analogous enzymes have different enzymatic behavior in different organisms. CBSs from the higher organisms contain a heme in an N-terminal domain. Though the presence of the heme, whose functions in CBSs have yet to be elucidated, is biochemically interesting, it hampers UV-vis absorption spectroscopy investigations of pyridoxal 5'-phosphate (PLP) species. CBS from Saccharomyces cerevisiae (yCBS) naturally lacks the heme-containing N-terminal domain, which makes it an ideal model for spectroscopic studies of the enzymological reaction catalyzed and allows structural studies of the basic yCBS catalytic core (yCBS-cc). Here we present the crystal structure of yCBS-cc, solved to 1.5 Å. Crystal structures of yCBS-cc in complex with enzymatic reaction intermediates have been captured, providing a structural basis for residues involved in catalysis. Finally, the structure of the yCBS-cc cofactor complex generated by incubation with an inhibitor shows apparent off-pathway chemistry not normally seen with CBS.


  • Organizational Affiliation

    Department of Biochemistry , Brandeis University , Waltham , Massachusetts 02454 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cystathionine beta-synthase375Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CYS4STR4YGR155WG6667
EC: 4.2.1.22
UniProt
Find proteins for P32582 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32582 
Go to UniProtKB:  P32582
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32582
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EVM (Subject of Investigation/LOI)
Query on EVM

Download Ideal Coordinates CCD File 
B [auth A]L-Serine, N-[[3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]-4-pyridinyl]methylene]
C11 H14 N2 O8 P
JFLJYKRWFQAEDK-QLKAYGNNSA-N
PGE
Query on PGE

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H [auth A],
I [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

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F [auth A],
G [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

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J [auth A],
K [auth A],
L [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

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C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

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D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.107α = 90
b = 81.107β = 90
c = 208.519γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXphasing
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM32415

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description