7ALQ

human GCH-GFRP inhibitory complex 7-deaza-GTP bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Biophysical and structural investigation of the regulation of human GTP cyclohydrolase I by its regulatory protein GFRP.

Ebenhoch, R.Bauer, M.Reinert, D.Kersting, A.Huber, S.Schmid, A.Hinz, I.Feiler, M.Muller, K.Nar, H.

(2021) J Struct Biol 213: 107691-107691

  • DOI: https://doi.org/10.1016/j.jsb.2020.107691
  • Primary Citation of Related Structures:  
    7ALQ

  • PubMed Abstract: 

    GTP Cyclohydrolase I (GCH1) catalyses the conversion of guanosine triphosphate (GTP) to dihydroneopterin triphosphate (H2NTP), the initiating step in the biosynthesis of tetrahydrobiopterin (BH4). BH4 functions as co-factor in neurotransmitter biosynthesis. BH4 homeostasis is a promising target to treat pain disorders in patients. The function of mammalian GCH1s is regulated by a metabolic sensing mechanism involving a regulator protein, GCH1 feedback regulatory protein (GFRP). Dependent on the relative cellular concentrations of effector ligands, BH4 and phenylalanine, GFRP binds GCH1 to form inhibited or activated complexes, respectively. We determined high-resolution structures of the ligand-free and -bound human GFRP and GCH1-GFRP complexes by X-ray crystallography. Highly similar binding modes of the substrate analogue 7-deaza-GTP to active and inhibited GCH1-GFRP complexes confirm a novel, dissociation rate-controlled mechanism of non-competitive inhibition to be at work. Further, analysis of all structures shows that upon binding of the effector molecules, the conformations of GCH1 or GFRP are altered and form highly complementary surfaces triggering a picomolar interaction of GFRP and GCH1 with extremely slow k off values, while GCH1-GFRP complexes rapidly disintegrate in absence of BH4 or phenylalanine. Finally, comparing behavior of full-length and N-terminally truncated GCH1 we conclude that the disordered GCH1 N-terminus does not have impact on complex formation and enzymatic activity. In summary, this comprehensive and methodologically diverse study helps to provide a better understanding of the regulation of GCH1 by GFRP and could thus stimulate research on GCH1 modulating drugs.


  • Organizational Affiliation

    Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397 Biberach an der Riss, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP cyclohydrolase 1
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
209Homo sapiensMutation(s): 0 
Gene Names: GCH1DYT5GCH
EC: 3.5.4.16
UniProt & NIH Common Fund Data Resources
Find proteins for P30793 (Homo sapiens)
Explore P30793 
Go to UniProtKB:  P30793
PHAROS:  P30793
GTEx:  ENSG00000131979 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30793
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GTP cyclohydrolase 1 feedback regulatory protein87Homo sapiensMutation(s): 0 
Gene Names: GCHFRGFRP
UniProt & NIH Common Fund Data Resources
Find proteins for P30047 (Homo sapiens)
Explore P30047 
Go to UniProtKB:  P30047
PHAROS:  P30047
GTEx:  ENSG00000137880 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30047
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QBQ (Subject of Investigation/LOI)
Query on QBQ

Download Ideal Coordinates CCD File 
AC [auth M]
BB [auth E]
DC [auth N]
EB [auth F]
FC [auth O]
AC [auth M],
BB [auth E],
DC [auth N],
EB [auth F],
FC [auth O],
HB [auth G],
IC [auth P],
KB [auth H],
LC [auth Q],
NB [auth I],
OC [auth R],
PA [auth A],
RB [auth J],
RC [auth S],
TA [auth B],
TB [auth K],
UC [auth T],
WA [auth C],
WB [auth L],
YA [auth D]
7-deaza-GTP
C11 H17 N4 O14 P3
NOXMCJDDSWCSIE-DAGMQNCNSA-N
HBI (Subject of Investigation/LOI)
Query on HBI

Download Ideal Coordinates CCD File 
BC [auth M]
CB [auth E]
FB [auth F]
GC [auth O]
IB [auth G]
BC [auth M],
CB [auth E],
FB [auth F],
GC [auth O],
IB [auth G],
JC [auth P],
LB [auth H],
MC [auth Q],
OB [auth I],
PB [auth I],
PC [auth R],
QA [auth A],
RA [auth A],
SC [auth S],
UA [auth B],
UB [auth K],
VC [auth T],
XB [auth L],
YB [auth L],
ZA [auth D]
7,8-DIHYDROBIOPTERIN
C9 H13 N5 O3
FEMXZDUTFRTWPE-DZSWIPIPSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
AB [auth E]
CC [auth N]
DB [auth F]
EC [auth O]
GB [auth G]
AB [auth E],
CC [auth N],
DB [auth F],
EC [auth O],
GB [auth G],
HC [auth P],
JB [auth H],
KC [auth Q],
MB [auth I],
NC [auth R],
OA [auth A],
QB [auth J],
QC [auth S],
SA [auth B],
SB [auth K],
TC [auth T],
VA [auth C],
VB [auth L],
XA [auth D],
ZB [auth M]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K (Subject of Investigation/LOI)
Query on K

Download Ideal Coordinates CCD File 
AD [auth e]
BD [auth f]
CD [auth g]
DD [auth h]
ED [auth i]
AD [auth e],
BD [auth f],
CD [auth g],
DD [auth h],
ED [auth i],
FD [auth j],
GD [auth k],
HD [auth l],
ID [auth m],
JD [auth n],
KD [auth o],
LD [auth p],
MD [auth q],
ND [auth r],
OD [auth s],
PD [auth t],
WC [auth a],
XC [auth b],
YC [auth c],
ZC [auth d]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.104α = 90
b = 185.418β = 97.94
c = 184.231γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-20
    Type: Initial release
  • Version 2.0: 2022-05-04
    Changes: Atomic model, Database references
  • Version 2.1: 2024-01-31
    Changes: Data collection, Refinement description