5X5H

Crystal structure of metB from Corynebacterium glutamicum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 

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This is version 1.2 of the entry. See complete history


Literature

Structural Insights into Substrate Specificity of Cystathionine gamma-Synthase from Corynebacterium glutamicum

Sagong, H.-Y.Kim, K.-J.

(2017) J Agric Food Chem 65: 6002-6008

  • DOI: 10.1021/acs.jafc.7b02391
  • Primary Citation of Related Structures:  
    5X5H

  • PubMed Abstract: 
  • Cystathionine γ-synthase (MetB) condenses O-acetyl-l-homoserine (OAHS) or O-succinyl-l-homoserine (OSHS) with cysteine to produce cystathionine. To investigate the molecular mechanisms and substrate specificity of MetB from Corynebacterium glutamicum (CgMetB), we determined its crystal structure at 1 ...

    Cystathionine γ-synthase (MetB) condenses O-acetyl-l-homoserine (OAHS) or O-succinyl-l-homoserine (OSHS) with cysteine to produce cystathionine. To investigate the molecular mechanisms and substrate specificity of MetB from Corynebacterium glutamicum (CgMetB), we determined its crystal structure at 1.5 Å resolution. The pyridoxal phosphate cofactor is covalently bound to Lys204 via a Schiff base linkage in the deep cavity. Superposition with the structure of MetB from Nicotiana tabacum in complex with its inhibitor dl-(E)-2-amino-5-phosphono-3-pentenoic acid revealed that Thr347 from the β10-β11 connecting loop, located at the entrance of the active site, is speculated to be a main contributor for stabilization of the acetyl group of OAHS. Moreover, on the basis of structural comparison of CgMetB with EcMetB utilizing OSHS as a main substrate, we propose that the conformation of the β10-β11 connecting loops determines the size and shape of the acetyl- or succinyl-group binding site and ultimately determines the substrate specificity of MetBs toward OAHS or OSHS.


    Organizational Affiliation

    KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University , Daehak-ro 80, Buk-ku, Daegu 702-701, Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cystathionine beta-lyases/cystathionine gamma-synthasesA392Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: Cgl2446
EC: 2.5.1.48
UniProt
Find proteins for Q79VD9 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
Explore Q79VD9 
Go to UniProtKB:  Q79VD9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ79VD9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download Ideal Coordinates CCD File 
B [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.574α = 90
b = 149.851β = 90
c = 161.858γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data processing
MOLREPphasing
HKL-2000data scaling
HKLdata reduction

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2017-08-16
    Changes: Database references
  • Version 1.2: 2020-09-16
    Changes: Derived calculations, Structure summary