4IYO

Crystal structure of cystathionine gamma lyase from Xanthomonas oryzae pv. oryzae (XometC) in complex with E-site serine, A-site serine, A-site external aldimine structure with aminoacrylate and A-site iminopropionate intermediates


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

PLP undergoes conformational changes during the course of an enzymatic reaction.

Ngo, H.P.Cerqueira, N.M.Kim, J.K.Hong, M.K.Fernandes, P.A.Ramos, M.J.Kang, L.W.

(2014) Acta Crystallogr D Biol Crystallogr 70: 596-606

  • DOI: https://doi.org/10.1107/S1399004713031283
  • Primary Citation of Related Structures:  
    4IXS, 4IXZ, 4IY7, 4IYO

  • PubMed Abstract: 

    Numerous enzymes, such as the pyridoxal 5'-phosphate (PLP)-dependent enzymes, require cofactors for their activities. Using X-ray crystallography, structural snapshots of the L-serine dehydratase catalytic reaction of a bacterial PLP-dependent enzyme were determined. In the structures, the dihedral angle between the pyridine ring and the Schiff-base linkage of PLP varied from 18° to 52°. It is proposed that the organic cofactor PLP directly catalyzes reactions by active conformational changes, and the novel catalytic mechanism involving the PLP cofactor was confirmed by high-level quantum-mechanical calculations. The conformational change was essential for nucleophilic attack of the substrate on PLP, for concerted proton transfer from the substrate to the protein and for directing carbanion formation of the substrate. Over the whole catalytic cycle, the organic cofactor catalyzes a series of reactions, like the enzyme. The conformational change of the PLP cofactor in catalysis serves as a starting point for identifying the previously unknown catalytic roles of organic cofactors.


  • Organizational Affiliation

    Department of Biological Sciences, Konkuk University, 1 Hwayang dong, Gwangjin-gu, Seoul 143-701, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cystathionine gamma-lyase-like protein397Xanthomonas oryzae pv. oryzae KACC 10331Mutation(s): 0 
Gene Names: metBXOCGLXOO0778
EC: 4.4.1.1
UniProt
Find proteins for Q5H4T8 (Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85))
Explore Q5H4T8 
Go to UniProtKB:  Q5H4T8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5H4T8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cystathionine gamma-lyase-like protein, LYS201A modified
B, C, D
397Xanthomonas oryzae pv. oryzae KACC 10331Mutation(s): 0 
Gene Names: metBXOCGLXOO0778
EC: 4.4.1.1
UniProt
Find proteins for Q5H4T8 (Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85))
Explore Q5H4T8 
Go to UniProtKB:  Q5H4T8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5H4T8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0JO
Query on 0JO

Download Ideal Coordinates CCD File 
H [auth A]2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid
C11 H13 N2 O7 P
BHIGINKEEFZJGX-YIXHJXPBSA-N
SER
Query on SER

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C],
O [auth D],
P [auth D]
SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-REOHCLBHSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
N [auth C],
Q [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
PYR
Query on PYR

Download Ideal Coordinates CCD File 
K [auth B]PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
NAK
Query on NAK

Download Ideal Coordinates CCD File 
J [auth B],
M [auth C]
AMINO-ACRYLATE
C3 H5 N O2
DUAWRLXHCUAWMK-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
B, C, D
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.319α = 90
b = 86.344β = 90
c = 226.344γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data 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: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-02-26
    Changes: Database references
  • Version 1.2: 2017-05-03
    Changes: Non-polymer description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection