3B1D

Crystal structure of betaC-S lyase from Streptococcus anginosus in complex with L-serine: External aldimine form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural insights into catalysis by beta C-S lyase from Streptococcus anginosus

Kezuka, Y.Yoshida, Y.Nonaka, T.

(2012) Proteins 80: 2447-2458

  • DOI: 10.1002/prot.24129
  • Primary Citation of Related Structures:  
    3B1C, 3B1D, 3B1E

  • PubMed Abstract: 
  • Hydrogen sulfide (H(2)S) is a causative agent of oral malodor and may play an important role in the pathogenicity of oral bacteria such as Streptococcus anginosus. In this microorganism, H(2)S production is associated with βC-S lyase (Lcd) encoded by lcd gene, which is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the α,β-elimination of sulfur-containing amino acids ...

    Hydrogen sulfide (H(2)S) is a causative agent of oral malodor and may play an important role in the pathogenicity of oral bacteria such as Streptococcus anginosus. In this microorganism, H(2)S production is associated with βC-S lyase (Lcd) encoded by lcd gene, which is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the α,β-elimination of sulfur-containing amino acids. When Lcd acts on L-cysteine, H(2)S is produced along with pyruvate and ammonia. To understand the H(2)S-producing mechanism of Lcd in detail, we determined the crystal structures of substrate-free Lcd (internal aldimine form) and two reaction intermediate complexes (external aldimine and α-aminoacrylate forms). The formation of intermediates induced little changes in the overall structure of the enzyme and in the active site residues, with the exception of Lys234, a PLP-binding residue. Structural and mutational analyses highlighted the importance of the active site residues Tyr60, Tyr119, and Arg365. In particular, Tyr119 forms a hydrogen bond with the side chain oxygen atom of L-serine, a substrate analog, in the external aldimine form suggesting its role in the recognition of the sulfur atom of the true substrate (L-cysteine). Tyr119 also plays a role in fixing the PLP cofactor at the proper position during catalysis through binding with its side chain. Finally, we partly modified the catalytic mechanism known for cystalysin, a βC-S lyase from Treponema denticola, and proposed an improved mechanism, which seems to be common to the βC-S lyases from oral bacteria.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of betaC-S lyases from two oral Streptococci
      Kezuka, Y., Yoshida, Y., Nonaka, T.
      (2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 874
    • Molecular and enzymatic characterization of betaC-S lyase in Streptococcus constellatus
      Yoshida, Y., Ito, S., Sasaki, T., Kishi, M., Kurota, M., Suwabe, A., Kunimatsu, K., Kato, H.
      (2008) Oral Microbiol Immunol 23: 245
    • Differences in the betaC-S lyase activities of viridans group streptococci
      Yoshida, Y., Negishi, M., Amano, A., Oho, T., Nakano, Y.
      (2003) Biochem Biophys Res Commun 300: 55
    • lcd from Streptococcus anginosus encodes a C-S lyase with alpha,beta-elimination activity that degrades L-cysteine
      Yoshida, Y., Nakano, Y., Amano, A., Yoshimura, M., Fukamachi, H., Oho, T., Koga, T.
      (2002) Microbiology (N Y) 148: 3961

    Organizational Affiliation

    Department of Structural Biology, School of Pharmacy, Iwate Medical University, Yahaba, Iwate, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BetaC-S lyaseA, B, C, D392Streptococcus anginosusMutation(s): 0 
Gene Names: lcd
EC: 4.4.1.8
UniProt
Find proteins for A6BMJ3 (Streptococcus anginosus)
Explore A6BMJ3 
Go to UniProtKB:  A6BMJ3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLS (Subject of Investigation/LOI)
Query on PLS

Download Ideal Coordinates CCD File 
F [auth A], K [auth B], P [auth C], U [auth D][3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE
C11 H17 N2 O8 P
ODVKKQWXKRZJLG-VIFPVBQESA-N
 Ligand Interaction
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
E [auth A], O [auth C]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
EPE
Query on EPE

Download Ideal Coordinates CCD File 
G [auth A] , H [auth A] , I [auth A] , L [auth B] , M [auth B] , Q [auth C] , R [auth C] , S [auth C] , 
G [auth A],  H [auth A],  I [auth A],  L [auth B],  M [auth B],  Q [auth C],  R [auth C],  S [auth C],  V [auth D],  W [auth D],  X [auth D]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth A], N [auth B], T [auth C], Y [auth D]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.965α = 90
b = 111.302β = 90
c = 217.193γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
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: 2012-06-27
    Type: Initial release
  • Version 1.1: 2014-01-22
    Changes: Database references
  • Version 1.2: 2017-10-11
    Changes: Advisory, Refinement description