7D1H | pdb_00007d1h

Crystal structure of Ixodes scapularis glutaminyl cyclase with D238A mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 
    0.217 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7D1H

This is version 1.3 of the entry. See complete history

Literature

A Unique Carboxylic-Acid Hydrogen-Bond Network (CAHBN) Confers Glutaminyl Cyclase Activity on M28 Family Enzymes.

Huang, K.F.Huang, J.S.Wu, M.L.Hsieh, W.L.Hsu, K.C.Hsu, H.L.Ko, T.P.Wang, A.H.

(2021) J Mol Biology 433: 166960-166960

  • DOI: https://doi.org/10.1016/j.jmb.2021.166960
  • Primary Citation Related Structures: 
    7D17, 7D18, 7D1B, 7D1D, 7D1E, 7D1H, 7D1N, 7D1P, 7D1Y, 7D21, 7D23, 7D2B, 7D2D, 7D2I, 7D2J

  • PubMed Abstract: 

    Proteins with sequence or structure similar to those of di-Zn exopeptidases are usually classified as the M28-family enzymes, including the mammalian-type glutaminyl cyclases (QCs). QC catalyzes protein N-terminal pyroglutamate formation, a posttranslational modification important under many physiological and pathological conditions, and is a drug target for treating neurodegenerative diseases, cancers and inflammatory disorders. Without functional characterization, mammalian QCs and their orthologs remain indistinguishable at the sequence and structure levels from other M28-family proteins, leading to few reported QCs. Here, we show that a low-barrier carboxylic-acid hydrogen-bond network (CAHBN) is required for QC activity and discriminates QCs from M28-family peptidases. We demonstrate that the CAHBN-containing M28 peptidases deposited in the PDB are indeed QCs. Our analyses identify several thousands of QCs from the three domains of life, and we enzymatically and structurally characterize several. For the first time, the interplay between a CAHBN and the binuclear metal-binding center of mammalian QCs is made clear. We found that the presence or absence of CAHBN is a key discriminator for the formation of either the mono-Zn QCs or the di-Zn exopeptidases. Our study helps explain the possible roles of QCs in life.


  • Organizational Affiliation
    • Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan. Electronic address: huangkf@gate.sinica.edu.tw.

Macromolecule Content 

  • Total Structure Weight: 38.31 kDa 
  • Atom Count: 3,019 
  • Modeled Residue Count: 326 
  • Deposited Residue Count: 329 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutaminyl-peptide cyclotransferase329Ixodes scapularisMutation(s): 0 
Gene Names: 8042451IscW_ISCW023264
EC: 2.3.2.5
UniProt
Find proteins for B7QK46 (Ixodes scapularis)
Explore B7QK46 
Go to UniProtKB:  B7QK46
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7QK46
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free:  0.217 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.534α = 90
b = 71.403β = 90
c = 80.225γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academia Sinica (Taiwan)TaiwanAS-KPQ-109-ITAR-11, AS-SUMMIT-109, AS-KPQ-109-TPP2, AS-KPQ-109-TSPA

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2021-05-05
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary