2QQC

E109Q mutant of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of the N47A and E109Q mutant proteins of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii.

Soriano, E.V.McCloskey, D.E.Kinsland, C.Pegg, A.E.Ealick, S.E.

(2008) Acta Crystallogr D Biol Crystallogr 64: 377-382

  • DOI: 10.1107/S0907444908000474
  • Primary Citation of Related Structures:  
    2QQC, 2QQD

  • PubMed Abstract: 
  • Pyruvoyl-dependent arginine decarboxylase (PvlArgDC) catalyzes the first step of the polyamine-biosynthetic pathway in plants and some archaebacteria. The pyruvoyl group of PvlArgDC is generated by an internal autoserinolysis reaction at an absolutely conserved serine residue in the proenzyme, resulting in two polypeptide chains ...

    Pyruvoyl-dependent arginine decarboxylase (PvlArgDC) catalyzes the first step of the polyamine-biosynthetic pathway in plants and some archaebacteria. The pyruvoyl group of PvlArgDC is generated by an internal autoserinolysis reaction at an absolutely conserved serine residue in the proenzyme, resulting in two polypeptide chains. Based on the native structure of PvlArgDC from Methanococcus jannaschii, the conserved residues Asn47 and Glu109 were proposed to be involved in the decarboxylation and autoprocessing reactions. N47A and E109Q mutant proteins were prepared and the three-dimensional structure of each protein was determined at 2.0 A resolution. The N47A and E109Q mutant proteins showed reduced decarboxylation activity compared with the wild-type PvlArgDC. These residues may also be important for the autoprocessing reaction, which utilizes a mechanism similar to that of the decarboxylation reaction.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850-1301, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyruvoyl-dependent arginine decarboxylase (EC 4.1.1.19) (PvlArgDC)A, C, E, G, I, K53Methanocaldococcus jannaschiiMutation(s): 0 
Gene Names: pdaD
EC: 4.1.1.19
UniProt
Find proteins for Q57764 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q57764 
Go to UniProtKB:  Q57764
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pyruvoyl-dependent arginine decarboxylase (EC 4.1.1.19) (PvlArgDC)B, D, F, H, J, L112Methanocaldococcus jannaschiiMutation(s): 1 
Gene Names: pdaD
EC: 4.1.1.19
UniProt
Find proteins for Q57764 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q57764 
Go to UniProtKB:  Q57764
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AG2
Query on AG2

Download Ideal Coordinates CCD File 
AA [auth K], M [auth A], N [auth A], S [auth E], W [auth I], X [auth I]AGMATINE
C5 H14 N4
QYPPJABKJHAVHS-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
P [auth B], Q [auth C], T [auth E], Y [auth I](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
PYR
Query on PYR

Download Ideal Coordinates CCD File 
BA [auth L], O [auth B], R [auth D], U [auth F], V [auth H], Z [auth J]PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.108α = 90
b = 92.81β = 95.11
c = 85.707γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations