4L9Z

Crystal Structure of Rhodobacter sphaeroides malyl-CoA lyase in complex with magnesium, oxalate, and CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

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Ligand Structure Quality Assessment 


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Literature

The crystal structures of the tri-functional Chloroflexus aurantiacus and bi-functional Rhodobacter sphaeroides malyl-CoA lyases and comparison with CitE-like superfamily enzymes and malate synthases.

Zarzycki, J.Kerfeld, C.A.

(2013) BMC Struct Biol 13: 28-28

  • DOI: https://doi.org/10.1186/1472-6807-13-28
  • Primary Citation of Related Structures:  
    4L7Z, 4L80, 4L9Y, 4L9Z

  • PubMed Abstract: 

    Malyl-CoA lyase (MCL) is a promiscuous carbon-carbon bond lyase that catalyzes the reversible cleavage of structurally related Coenzyme A (CoA) thioesters. This enzyme plays a crucial, multifunctional role in the 3-hydroxypropionate bi-cycle for autotrophic CO2 fixation in Chloroflexus aurantiacus. A second, phylogenetically distinct MCL from Rhodobacter sphaeroides is involved in the ethylmalonyl-CoA pathway for acetate assimilation. Both MCLs belong to the large superfamily of CitE-like enzymes, which includes the name-giving β-subunit of citrate lyase (CitE), malyl-CoA thioesterases and other enzymes of unknown physiological function. The CitE-like enzyme superfamily also bears sequence and structural resemblance to the malate synthases. All of these different enzymes share highly conserved catalytic residues, although they catalyze distinctly different reactions: C-C bond formation and cleavage, thioester hydrolysis, or both (the malate synthases).


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Plant Research Laboratories, Michigan State University, Plant Biology Building, 612 Wilson Road, East Lansing, MI 48824, USA. ckerfeld@lbl.gov.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Malyl-CoA lyase
A, B, C, D, E
A, B, C, D, E, F
339Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Gene Names: mcl1RHOS4_03500RSP_1771
EC: 4.1.3.24
UniProt
Find proteins for Q3J5L6 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3J5L6 
Go to UniProtKB:  Q3J5L6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3J5L6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
M [auth C]
P [auth D]
S [auth E]
G [auth A],
J [auth B],
M [auth C],
P [auth D],
S [auth E],
V [auth F]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
OXL
Query on OXL

Download Ideal Coordinates CCD File 
H [auth A]
K [auth B]
N [auth C]
Q [auth D]
T [auth E]
H [auth A],
K [auth B],
N [auth C],
Q [auth D],
T [auth E],
W [auth F]
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
O [auth C]
R [auth D]
U [auth E]
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
X [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 221.509α = 90
b = 221.509β = 90
c = 96.262γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-04
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description