2FJT

Adenylyl cyclase class iv from Yersinia pestis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.901 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the class IV adenylyl cyclase reveals a novel fold

Gallagher, D.T.Smith, N.N.Kim, S.-K.Heroux, A.Robinson, H.Reddy, P.T.

(2006) J.Mol.Biol. 362: 114-122

  • DOI: 10.1016/j.jmb.2006.07.008

  • PubMed Abstract: 
  • The crystal structure of the class IV adenylyl cyclase (AC) from Yersinia pestis (Yp) is reported at 1.9 A resolution. The class IV AC fold is distinct from the previously described folds for class II and class III ACs. The dimeric AC-IV folds into a ...

    The crystal structure of the class IV adenylyl cyclase (AC) from Yersinia pestis (Yp) is reported at 1.9 A resolution. The class IV AC fold is distinct from the previously described folds for class II and class III ACs. The dimeric AC-IV folds into an antiparallel eight-stranded barrel whose connectivity has been seen in only three previous structures: yeast RNA triphosphatase and two proteins of unknown function from Pyrococcus furiosus and Vibrio parahaemolyticus. Eight highly conserved ionic residues E10, E12, K14, R63, K76, K111, D126, and E136 lie in the barrel core and form the likely binding sites for substrate and divalent cations. A phosphate ion is observed bound to R63, K76, K111, and R113 near the center of the conserved cluster. Unlike the AC-II and AC-III active sites that utilize two-Asp motifs for cation binding, the AC-IV active site is relatively enriched in glutamate and features an ExE motif as its most conserved element. Homologs of Y. pestis AC-IV, including human thiamine triphosphatase, span the three kingdoms of life and delineate an ancient family of phosphonucleotide processing enzymes.


    Related Citations: 
    • Crystallization of the class IV adenylyl cyclase from Yersinia pestis
      Smith, N.N.,Kim, S.-K.,Reddy, P.T.,Gallagher, D.T.
      (2006) Acta Crystallogr.,Sect.F 62: --


    Organizational Affiliation

    Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8310, USA. travis.gallagher@nist.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenylyl cyclase class IV
A, B
182Yersinia pestisMutation(s): 0 
Gene Names: cyaB
EC: 4.6.1.1
Find proteins for A0A384LKY8 (Yersinia pestis)
Go to UniProtKB:  A0A384LKY8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSX
Query on CSX
A, B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.901 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.212 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 33.529α = 88.89
b = 35.548β = 82.63
c = 71.985γ = 65.47
Software Package:
Software NamePurpose
CrystalCleardata reduction
AMoREphasing
CrystalCleardata collection
CrystalCleardata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation