5ZI9

Crystal structure of type-II LOG from Streptomyces coelicolor A3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and biochemical characterization of the type-II LOG protein from Streptomyces coelicolor A3.

Seo, H.Kim, K.J.

(2018) Biochem Biophys Res Commun 499: 577-583

  • DOI: 10.1016/j.bbrc.2018.03.193
  • Primary Citation of Related Structures:  
    5ZI9

  • PubMed Abstract: 
  • Streptomyces coelicolor A3 contains Sc5140, a gene coding for poorly understood bacterial LOG-like protein. In this study, we determined the crystal structure of Sc5140 and found it resembles the overall structure of other type-II LOGs. In addition, Sc5140 exhibited phosphoribohydrolase activity against adenosine monophosphate (AMP), indicating that it had the same function as known type-II LOGs ...

    Streptomyces coelicolor A3 contains Sc5140, a gene coding for poorly understood bacterial LOG-like protein. In this study, we determined the crystal structure of Sc5140 and found it resembles the overall structure of other type-II LOGs. In addition, Sc5140 exhibited phosphoribohydrolase activity against adenosine monophosphate (AMP), indicating that it had the same function as known type-II LOGs. Based on these results, we designated Sc5140 as ScLOGII. We performed docking calculations of AMP into the ScLOGII structure, which suggested the mode of binding for type-II LOG with their AMP substrate. The ScLOGII structure uniquely exhibited a long tail-like structure at the N-terminus that was involved in hexamerization of the protein; the disordered N-terminal region (DNR). Truncation of DNR in ScLOGII negatively affected both the phosphoribohydrolase activity and the oligomerization of the protein, suggesting that this region functioned in enzyme stabilization. However, results from truncation experiments using ScLOGII and CgLOGII, a type-II LOG homologue from Corynebacterium glutamicum, were quite different, leaving uncertainty regarding the general functions of DNR in type-II LOGs. Overall, the current structural work may help in understand the significance of type-II LOG protein at the molecular level.


    Organizational Affiliation

    School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea. Electronic address: kkim@knu.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytokinin riboside 5'-monophosphate phosphoribohydrolaseA, B, C, D260Streptomyces coelicolor A3(2)Mutation(s): 0 
Gene Names: SCO5140
EC: 3.2.2
UniProt
Find proteins for Q9FBL8 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9FBL8 
Go to UniProtKB:  Q9FBL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FBL8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
L [auth B],
P [auth C],
T [auth D],
G [auth A],
K [auth B],
L [auth B],
P [auth C],
T [auth D],
U [auth D]
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
Q [auth C],
R [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
J [auth B],
M [auth B],
N [auth C],
E [auth A],
F [auth A],
J [auth B],
M [auth B],
N [auth C],
O [auth C],
S [auth D],
V [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 206.768α = 90
b = 206.768β = 90
c = 206.768γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2018-03-14 
  • Released Date: 2018-04-18 
  • Deposition Author(s): Seo, H., Kim, K.-J.

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-05-02
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.2: 2020-09-16
    Changes: Structure summary