5ZLP

Crystal structure of glutamine synthetase from helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural Analysis of Glutamine Synthetase from Helicobacter pylori.

Joo, H.K.Park, Y.W.Jang, Y.Y.Lee, J.Y.

(2018) Sci Rep 8: 11657-11657

  • DOI: https://doi.org/10.1038/s41598-018-30191-5
  • Primary Citation of Related Structures:  
    5ZLI, 5ZLP

  • PubMed Abstract: 

    Glutamine synthetase (GS) is an enzyme that regulates nitrogen metabolism and synthesizes glutamine via glutamate, ATP, and ammonia. GS is a homo-oligomeric protein of eight, ten, or twelve subunits, and each subunit-subunit interface has its own active site. GS can be divided into GS I, GS II, and GS III. GS I and GS III form dodecamer in bacteria and archaea, whereas GS II form decamer in eukaryotes. GS I can be further subdivided into GS I-α and GS I-β according to its sequence and regulatory mechanism. GS is an essential protein for the survival of Helicobacter pylori which its infection could promote gastroduodenal diseases. Here, we determined the crystal structures of the GS from H. pylori (Hpy GS) in its apo- and substrate-bound forms at 2.8 Å and 2.9 Å resolution, respectively. Hpy GS formed a dodecamer composed of two hexameric rings stacked face-to-face. Hpy GS, which belongs to GS I, cannot be clearly classified as either GS I-α or GS I-β based on its sequence and regulatory mechanism. In this study, we propose that Hpy GS could be classified as a new GS-I subfamily and provide structural information on the apo- and substrate-bound forms of the protein.


  • Organizational Affiliation

    Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamine synthetase481Helicobacter pylori 26695Mutation(s): 0 
Gene Names: glnAHP_0512
EC: 6.3.1.2
UniProt
Find proteins for P94845 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P94845 
Go to UniProtKB:  P94845
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP94845
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
CA [auth G]
M [auth A]
N [auth B]
O [auth C]
R [auth F]
CA [auth G],
M [auth A],
N [auth B],
O [auth C],
R [auth F],
W [auth K]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth L]
DA [auth I]
P [auth D]
Q [auth E]
S [auth H]
AA [auth L],
DA [auth I],
P [auth D],
Q [auth E],
S [auth H],
T [auth J]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
P3P
Query on P3P

Download Ideal Coordinates CCD File 
Y [auth L](2S)-2-AMINO-4-[METHYL(PHOSPHONOOXY)PHOSPHORYL]BUTANOIC ACID
C5 H13 N O7 P2
UXRZHSKRCMUNIN-YZSVAWROSA-N
PPQ
Query on PPQ

Download Ideal Coordinates CCD File 
EA [auth I],
U [auth J],
X [auth K]
PHOSPHINOTHRICIN
C5 H12 N O4 P
IAJOBQBIJHVGMQ-BYPYZUCNSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth L],
FA [auth I],
V [auth J],
Z [auth L]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 234.409α = 90
b = 135.167β = 91.61
c = 203.08γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2017R1D1A1B03032109
Korea, Republic Of710013-03-1-SB120

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references, Derived calculations