6K37

Crystal structure of BioU (K124A) from Synechocystis sp.PCC6803 in complex with NAD+ and the analog of reaction intermediate, 3-(1-aminoethyl)-nonanedioic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria.

Sakaki, K.Ohishi, K.Shimizu, T.Kobayashi, I.Mori, N.Matsuda, K.Tomita, T.Watanabe, H.Tanaka, K.Kuzuyama, T.Nishiyama, M.

(2020) Nat Chem Biol 16: 415-422

  • DOI: https://doi.org/10.1038/s41589-019-0461-9
  • Primary Citation of Related Structures:  
    6IR4, 6ITD, 6K36, 6K37, 6K38

  • PubMed Abstract: 

    In biotin biosynthesis, the conversion of pimeloyl intermediates to biotin is catalyzed by a universal set of four enzymes: BioF, BioA, BioD and BioB. We found that the gene homologous to bioA, the product of which is involved in the conversion of 8-amino-7-oxononanoate (AON) to 7,8-diaminononanoate (DAN), is missing in the genome of the cyanobacterium Synechocystis sp. PCC 6803. We provide structural and biochemical evidence showing that a novel dehydrogenase, BioU, is involved in biotin biosynthesis and functionally replaces BioA. This enzyme catalyzes three reactions: formation of covalent linkage with AON to yield a BioU-DAN conjugate at the ε-amino group of Lys124 of BioU using NAD(P)H, carboxylation of the conjugate to form BioU-DAN-carbamic acid, and release of DAN-carbamic acid using NAD(P) + . In this biosynthetic pathway, BioU is a suicide enzyme that loses the Lys124 amino group after a single round of reaction.


  • Organizational Affiliation

    Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Slr0355 protein353Synechocystis sp. PCC 6803Mutation(s): 1 
Gene Names: slr0355
UniProt
Find proteins for Q55650 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore Q55650 
Go to UniProtKB:  Q55650
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ55650
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
B [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
CWL (Subject of Investigation/LOI)
Query on CWL

Download Ideal Coordinates CCD File 
C [auth A](3R)-3-[(1R)-1-azanylethyl]nonanedioic acid
C11 H21 N O4
NHQUUILSXUJSSP-RKDXNWHRSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.178 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.414α = 90
b = 70.414β = 90
c = 98.778γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
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: 2020-02-26
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description