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PDBsum entry 1mt1

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protein ligands Protein-protein interface(s) links
Lyase PDB id
1mt1
Jmol
Contents
Protein chains
46 a.a. *
(+ 0 more) 113 a.a. *
48 a.a. *
50 a.a. *
41 a.a. *
Ligands
AG2 ×5
Waters ×454
* Residue conservation analysis
PDB id:
1mt1
Name: Lyase
Title: The crystal structure of pyruvoyl-dependent arginine decarboxylase from methanococcus jannaschii
Structure: Pyruvoyl-dependent arginine decarboxylase beta chain. Chain: a, c, e, g, i, k. Engineered: yes. Pyruvoyl-dependent arginine decarboxylase alpha chain. Chain: b, d, f, h, j, l. Engineered: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: mj0316. Expressed in: escherichia coli. Expression_system_taxid: 562. (Stratagene).
Biol. unit: Hexamer (from PQS)
Resolution:
2.20Å     R-factor:   0.190     R-free:   0.229
Authors: W.D.Tolbert,D.E.Graham,R.H.White,S.E.Ealick
Key ref:
W.D.Tolbert et al. (2003). Pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii: crystal structures of the self-cleaved and S53A proenzyme forms. Structure, 11, 285-294. PubMed id: 12623016 DOI: 10.1016/S0969-2126(03)00026-1
Date:
20-Sep-02     Release date:   25-Mar-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q57764  (PDAD_METJA) -  Pyruvoyl-dependent arginine decarboxylase
Seq:
Struc:
165 a.a.
46 a.a.
Protein chains
Pfam   ArchSchema ?
Q57764  (PDAD_METJA) -  Pyruvoyl-dependent arginine decarboxylase
Seq:
Struc:
165 a.a.
113 a.a.*
Protein chain
Pfam   ArchSchema ?
Q57764  (PDAD_METJA) -  Pyruvoyl-dependent arginine decarboxylase
Seq:
Struc:
165 a.a.
48 a.a.
Protein chains
Pfam   ArchSchema ?
Q57764  (PDAD_METJA) -  Pyruvoyl-dependent arginine decarboxylase
Seq:
Struc:
165 a.a.
50 a.a.
Protein chain
Pfam   ArchSchema ?
Q57764  (PDAD_METJA) -  Pyruvoyl-dependent arginine decarboxylase
Seq:
Struc:
165 a.a.
41 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L: E.C.4.1.1.19  - Arginine decarboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-arginine = agmatine + CO2
L-arginine
=
agmatine
Bound ligand (Het Group name = AG2)
corresponds exactly
+ CO(2)
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cellular amino acid metabolic process   2 terms 
  Biochemical function     carboxy-lyase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(03)00026-1 Structure 11:285-294 (2003)
PubMed id: 12623016  
 
 
Pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii: crystal structures of the self-cleaved and S53A proenzyme forms.
W.D.Tolbert, D.E.Graham, R.H.White, S.E.Ealick.
 
  ABSTRACT  
 
The three-dimensional structure of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii was determined at 1.4 A resolution. The pyruvoyl group of arginine decarboxylase is generated by an autocatalytic internal serinolysis reaction at Ser53 in the proenzyme resulting in two polypeptide chains. The structure of the nonprocessing S53A mutant was also determined. The active site of the processed enzyme unexpectedly contained the reaction product agmatine. The crystal structure confirms that arginine decarboxylase is a homotrimer. The protomer fold is a four-layer alphabetabetaalpha sandwich with topology similar to pyruvoyl-dependent histidine decarboxylase. Highly conserved residues Asn47, Ser52, Ser53, Ile54, and Glu109 are proposed to play roles in the self-processing reaction. Agmatine binding residues include the C terminus of the beta chain (Ser52) from one protomer and the Asp35 side chain and the Gly44 and Val46 carbonyl oxygen atoms from an adjacent protomer. Glu109 is proposed to play a catalytic role in the decarboxylation reaction.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Stereo View of the Active Site of PvlArgDCThe product agamatine and key residues are shown as ball-and-stick models. Electron density is shown for the agmatine molecule and the pyruvoyl group. Key hydrogen bonds between agmatine and the protein are shown as dashed lines and the donor-acceptor distances are labeled. The figure was generated with BOBSCRIPT [44 and 45] and Raster3D [46].
 
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 285-294) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21208300 H.Trip, N.L.Mulder, F.P.Rattray, and J.S.Lolkema (2011).
HdcB, a novel enzyme catalysing maturation of pyruvoyl-dependent histidine decarboxylase.
  Mol Microbiol, 79, 861-871.  
19997761 S.Bale, and S.E.Ealick (2010).
Structural biology of S-adenosylmethionine decarboxylase.
  Amino Acids, 38, 451-460.  
19607664 T.N.Giles, D.J.Fisher, and D.E.Graham (2009).
Independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in Chlamydia trachomatis serovar L2 and D strains.
  BMC Evol Biol, 9, 166.  
  19255484 X.Y.Liu, J.Lei, X.Liu, X.D.Su, and L.Li (2009).
Preliminary X-ray crystallographic studies of Bacillus subtilis SpeA protein.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 282-284.  
18096851 L.L.Grochowski, and R.H.White (2008).
Promiscuous anaerobes: new and unconventional metabolism in methanogenic archaea.
  Ann N Y Acad Sci, 1125, 190-214.  
18650422 T.N.Giles, and D.E.Graham (2008).
Crenarchaeal arginine decarboxylase evolved from an S-adenosylmethionine decarboxylase enzyme.
  J Biol Chem, 283, 25829-25838.  
15150268 A.V.Toms, C.Kinsland, D.E.McCloskey, A.E.Pegg, and S.E.Ealick (2004).
Evolutionary links as revealed by the structure of Thermotoga maritima S-adenosylmethionine decarboxylase.
  J Biol Chem, 279, 33837-33846.
PDB codes: 1tlu 1tmi
14651609 F.Baunaure, P.Eldin, A.M.Cathiard, and H.Vial (2004).
Characterization of a non-mitochondrial type I phosphatidylserine decarboxylase in Plasmodium falciparum.
  Mol Microbiol, 51, 33-46.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.