7N1R

A novel and unique ATP hydrolysis to AMP by a human Hsp70 BiP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

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Ligand Structure Quality Assessment 


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Literature

A novel and unique ATP hydrolysis to AMP by a human Hsp70 Binding immunoglobin protein (BiP).

Li, H.Musayev, F.N.Yang, J.Su, J.Liu, Q.Wang, W.Fang, X.Zhou, L.Liu, Q.

(2021) Protein Sci 

  • DOI: 10.1002/pro.4267
  • Primary Citation of Related Structures:  
    7N1R

  • PubMed Abstract: 
  • Hsp70s are ubiquitous and highly conserved molecular chaperones. They play crucial roles in maintaining cellular protein homeostasis. It is well established that Hsp70s use the energy of ATP hydrolysis to ADP to power the chaperone activity regardless of the cellular locations and isoforms ...

    Hsp70s are ubiquitous and highly conserved molecular chaperones. They play crucial roles in maintaining cellular protein homeostasis. It is well established that Hsp70s use the energy of ATP hydrolysis to ADP to power the chaperone activity regardless of the cellular locations and isoforms. Binding immunoglobin protein (BiP), the major member of Hsp70s in the endoplasmic reticulum, is essential for protein folding and quality control. Unexpectedly, our structural analysis of BiP demonstrated a novel ATP hydrolysis to AMP during crystallization under the acidic conditions. Our biochemical studies confirmed this newly discovered ATP to AMP hydrolysis in solutions. Unlike the canonical ATP to ADP hydrolysis observed for Hsp70s, this ATP hydrolysis to AMP depends on the substrate-binding domain of BiP and is inhibited by the binding of a peptide substrate. Intriguingly, this ATP to AMP hydrolysis is unique to BiP, not shared by two representative Hsp70 proteins from the cytosol. Taken together, this novel and unique ATP to AMP hydrolysis may provide a potentially new direction for understanding the activity and cellular function of BiP.


    Organizational Affiliation

    Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endoplasmic reticulum chaperone BiPA, B606Homo sapiensMutation(s): 0 
Gene Names: HSPA5GRP78
EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P11021 (Homo sapiens)
Explore P11021 
Go to UniProtKB:  P11021
PHAROS:  P11021
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP (Subject of Investigation/LOI)
Query on AMP

Download Ideal Coordinates CCD File 
HA [auth B], Q [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
S [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth B], BA [auth B], G [auth A], H [auth A], U [auth B], Z [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PO4 (Subject of Investigation/LOI)
Query on PO4

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CA [auth B] , DA [auth B] , EA [auth B] , FA [auth B] , GA [auth B] , I [auth A] , IA [auth B] , J [auth A] , 
CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], I [auth A], IA [auth B], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], R [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], F [auth A], T [auth B], W [auth B], X [auth B], Y [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
P [auth A], V [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.988α = 84.88
b = 76.388β = 62.49
c = 79.917γ = 63.14
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM098592

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release