2ABM

Crystal Structure of Aquaporin Z Tetramer Reveals both Open and Closed Water-conducting Channels


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 

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This is version 2.0 of the entry. See complete history


Literature

Crystal Structure of AqpZ Tetramer Reveals Two Distinct Arg-189 Conformations Associated with Water Permeation through the Narrowest Constriction of the Water-conducting Channel.

Jiang, J.Daniels, B.V.Fu, D.

(2006) J Biol Chem 281: 454-460

  • DOI: https://doi.org/10.1074/jbc.M508926200
  • Primary Citation of Related Structures:  
    2ABM

  • PubMed Abstract: 

    AqpZ is a homotetramer of four water-conducting channels that facilitate rapid water movements across the plasma membrane of Escherichia coli. Here we report a 3.2 angstroms crystal structure of the tetrameric AqpZ (tAqpZ). All channel-lining residues in the four monomeric channels are found orientated in nearly identical positions with one marked exception at the narrowest channel constriction, where the side chain of a highly conserved Arg-189 adopts two distinct conformational orientations. In one of the four monomers, the guanidino group of Arg-189 points toward the periplasmic vestibule, opening up the constriction to accommodate the binding of a water molecule through a tridentate H-bond. In the other three monomers, the Arg-189 guanidino group bends over to form an H-bond with carbonyl oxygen of the Thr-183, thus occluding the channel. Therefore, the tAqpZ structure reveals two distinct Arg-189 confirmations associated with water permeation through the channel constrictions. Alternation between the two Arg-189 conformations disrupts continuous flow of water, thus regulating the open probability of the water pore. Further, the difference in Arg-189 displacements is correlated with a strong electron density found between the first transmembrane helices of two open channels, suggesting that the observed Arg-189 conformations are stabilized by asymmetrical subunit interactions in tAqpZ.


  • Organizational Affiliation

    Department of Biology, Brookhaven National Laboratory, Upton, New York 11973, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aquaporin Z
A, B, C, D, E
A, B, C, D, E, F, G, H
231Escherichia coliMutation(s): 0 
Gene Names: aqpZbniP
Membrane Entity: Yes 
UniProt
Find proteins for P60844 (Escherichia coli (strain K12))
Explore P60844 
Go to UniProtKB:  P60844
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60844
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEE
Query on PEE

Download Ideal Coordinates CCD File 
K [auth A]
O [auth B]
P [auth B]
U [auth E]
W [auth F]
K [auth A],
O [auth B],
P [auth B],
U [auth E],
W [auth F],
X [auth F],
Z [auth G]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
POQ
Query on POQ

Download Ideal Coordinates CCD File 
J [auth A]BIS(((3S,4S,5R,6R)-5-(ETHYL(PHOSPHORYLOXY))-3,4,6-TRIHYDROXY-TETRAHYDRO-2H-PYRAN-2-YL)METHYL) HYDROGEN PHOSPHATE
C16 H33 O20 P3
QTCHWELPTUAUQX-ASCZGESISA-N
AGA
Query on AGA

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BA [auth G],
S [auth C]
(1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE
C19 H36 O10 P
UQSXQYRZHMGKIE-DLBZAZTESA-M
BGL
Query on BGL

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I [auth A],
L [auth B],
M [auth B],
T [auth E]
2-O-octyl-beta-D-glucopyranose
C14 H28 O6
BVHPDIWLWHHJPD-RKQHYHRCSA-N
3PG
Query on 3PG

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AA [auth G],
R [auth C]
3-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
OSJPPGNTCRNQQC-UWTATZPHSA-N
PO4
Query on PO4

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N [auth B],
Q [auth C],
V [auth F],
Y [auth G]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.152α = 90
b = 119.152β = 90
c = 380.394γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-09-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-10-29
    Changes: Non-polymer description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 2.0: 2023-08-23
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary