5K2M

Bifunctional LysX/ArgX from Thermococcus kodakarensis with LysW-gamma-AAA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 3.1 of the entry. See complete history


Literature

Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic System.

Yoshida, A.Tomita, T.Atomi, H.Kuzuyama, T.Nishiyama, M.

(2016) J Biol Chem 291: 21630-21643

  • DOI: https://doi.org/10.1074/jbc.M116.743021
  • Primary Citation of Related Structures:  
    5K2M

  • PubMed Abstract: 

    We recently discovered a biosynthetic system using a novel amino group carrier protein called LysW for lysine biosynthesis via α-aminoadipate (AAA), and revealed that this system is also utilized in the biosynthesis of arginine by Sulfolobus In the present study, we focused on the biosynthesis of lysine and ornithine in the hyperthermophilic archaeon Thermococcus kodakarensis, and showed that their biosynthesis is accomplished by a single set of metabolic enzymes. We also determined the crystal structure of the LysX family protein from T. kodakarensis, which catalyzes the conjugation of LysW with either AAA or glutamate, in a complex with LysW-γ-AAA. This crystal structure is the first example to show how LysX recognizes AAA as a substrate and provides a structural basis for the bifunctionality of the LysX family protein from T. kodakarensis Based on comparisons with other LysX family proteins, we propose a mechanism for substrate recognition and its relationship with molecular evolution among LysX family proteins, which have different substrate specificities.


  • Organizational Affiliation

    From the Biotechnology Research Center, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RimK-related lysine biosynthesis protein
A, B, C, D, G
A, B, C, D, G, H, I, J
273Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK0278
UniProt
Find proteins for Q5JFW0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JFW0 
Go to UniProtKB:  Q5JFW0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JFW0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Probable lysine biosynthesis protein
E, F, K, L, M
E, F, K, L, M, N
53Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK0279
UniProt
Find proteins for Q5JFV9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JFV9 
Go to UniProtKB:  Q5JFV9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JFV9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
BA [auth G]
EA [auth H]
IA [auth I]
LA [auth J]
O [auth A]
BA [auth G],
EA [auth H],
IA [auth I],
LA [auth J],
O [auth A],
S [auth B],
W [auth C],
Y [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
UN1
Query on UN1

Download Ideal Coordinates CCD File 
KA [auth I]2-AMINOHEXANEDIOIC ACID
C6 H11 N O4
OYIFNHCXNCRBQI-BYPYZUCNSA-N
SO4
Query on SO4

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FA [auth H],
X [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PO4
Query on PO4

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CA [auth G],
JA [auth I],
MA [auth J],
P [auth A],
T [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

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AA [auth F],
Z [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
DA [auth G]
GA [auth H]
HA [auth H]
NA [auth J]
OA [auth J]
DA [auth G],
GA [auth H],
HA [auth H],
NA [auth J],
OA [auth J],
Q [auth A],
R [auth A],
U [auth B],
V [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
R0K
Query on R0K
E, F, K, L, M
E, F, K, L, M, N
L-PEPTIDE LINKINGC11 H18 N2 O7GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.15α = 90
b = 135.099β = 97.49
c = 136.977γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Data collection, Database references, Derived calculations
  • Version 2.0: 2023-04-05
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 3.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 3.1: 2023-11-29
    Changes: Refinement description