4W79

Crystal Structure of Human Protein N-terminal Glutamine Amidohydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3C9Q


Literature

Crystal structure of human protein N-terminal glutamine amidohydrolase, an initial component of the N-end rule pathway.

Park, M.S.Bitto, E.Kim, K.R.Bingman, C.A.Miller, M.D.Kim, H.J.Han, B.W.Phillips, G.N.

(2014) PLoS One 9: e111142-e111142

  • DOI: 10.1371/journal.pone.0111142
  • Primary Citation of Related Structures:  
    4W79

  • PubMed Abstract: 
  • The N-end rule states that half-life of protein is determined by their N-terminal amino acid residue. N-terminal glutamine amidohydrolase (Ntaq) converts N-terminal glutamine to glutamate by eliminating the amine group and plays an essential role in the N-end rule pathway for protein degradation ...

    The N-end rule states that half-life of protein is determined by their N-terminal amino acid residue. N-terminal glutamine amidohydrolase (Ntaq) converts N-terminal glutamine to glutamate by eliminating the amine group and plays an essential role in the N-end rule pathway for protein degradation. Here, we report the crystal structure of human Ntaq1 bound with the N-terminus of a symmetry-related Ntaq1 molecule at 1.5 Å resolution. The structure reveals a monomeric globular protein with alpha-beta-alpha three-layer sandwich architecture. The catalytic triad located in the active site, Cys-His-Asp, is highly conserved among Ntaq family and transglutaminases from diverse organisms. The N-terminus of a symmetry-related Ntaq1 molecule bound in the substrate binding cleft and the active site suggest possible substrate binding mode of hNtaq1. Based on our crystal structure of hNtaq1 and docking study with all the tripeptides with N-terminal glutamine, we propose how the peptide backbone recognition patch of hNtaq1 forms nonspecific interactions with N-terminal peptides of substrate proteins. Upon binding of a substrate with N-terminal glutamine, active site catalytic triad mediates the deamination of the N-terminal residue to glutamate by a mechanism analogous to that of cysteine proteases.


    Organizational Affiliation

    Department of Biochemistry, Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, Madison, Wisconsin, United States of America; Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein N-terminal glutamine amidohydrolaseA202Homo sapiensMutation(s): 4 
Gene Names: WDYHV1C8orf32NTAQ1
EC: 3.5.1 (PDB Primary Data), 3.5.1.122 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96HA8 (Homo sapiens)
Explore Q96HA8 
Go to UniProtKB:  Q96HA8
PHAROS:  Q96HA8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96HA8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
P [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3

Download Ideal Coordinates CCD File 
M [auth A],
N [auth A],
O [auth A]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.322α = 90
b = 64.039β = 90
c = 113.66γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54 GM074901

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence