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PDBsum entry 1gxy

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1gxy
Jmol
Contents
Protein chains
223 a.a. *
Ligands
GOL ×2
Waters ×498
* Residue conservation analysis
PDB id:
1gxy
Name: Transferase
Title: Crystal structure of the eucaryotic mono-adp-ribosyltransferase art2.2; crystal form a (p21)
Structure: T-cell ecto-adp-ribosyltransferase 2. Chain: a, b. Synonym: adp-ribosyltransferase, t-cell NAD(p)(+)--arginine adp-ribosyltransferase 2, t-cell mono(adp-ribosyl)transferase 2, alloantigen rt6.2, t-cell surface protein rt6.2. Engineered: yes
Source: Rattus norvegicus. Rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.71Å     R-factor:   0.187     R-free:   0.218
Authors: C.Mueller-Dieckmann,G.E.Schulz
Key ref:
C.Mueller-Dieckmann et al. (2002). Structure of the ecto-ADP-ribosyl transferase ART2.2 from rat. J Mol Biol, 322, 687-696. PubMed id: 12270706 DOI: 10.1016/S0022-2836(02)00818-5
Date:
15-Apr-02     Release date:   26-Sep-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P20974  (NAR2B_RAT) -  T-cell ecto-ADP-ribosyltransferase 2
Seq:
Struc:
275 a.a.
223 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.4.2.31  - NAD(+)--protein-arginine ADP-ribosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NAD+ + protein-L-arginine = nicotinamide + N(omega)-(ADP-D-ribosyl)- protein-L-arginine
NAD(+)
+ protein-L-arginine
= nicotinamide
+ N(omega)-(ADP-D-ribosyl)- protein-L-arginine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     protein ADP-ribosylation   1 term 
  Biochemical function     NAD(P)+-protein-arginine ADP-ribosyltransferase activity     1 term  

 

 
    reference    
 
 
DOI no: 10.1016/S0022-2836(02)00818-5 J Mol Biol 322:687-696 (2002)
PubMed id: 12270706  
 
 
Structure of the ecto-ADP-ribosyl transferase ART2.2 from rat.
C.Mueller-Dieckmann, H.Ritter, F.Haag, F.Koch-Nolte, G.E.Schulz.
 
  ABSTRACT  
 
The mammalian extracellular ADP-ribosyl transferases ART1 through ART5 are sequence-related to each other. Among them ART2 is involved in immuno regulation. The variant ART2.2 was expressed in the periplasm of Escherichia coli and crystallized. Its structure was determined by X-ray diffraction at 1.7A resolution in one crystal form and at slightly lower resolutions in two others. The active center was indicated by a ligated nicotinamide analogue, which also revealed a small induced-fit. The centerpiece of the chainfold of ART2.2 agrees with those of all bacterial ADP-ribosyl transferases. This correspondence and the nicotinamide position were used to model the binding structure of the whole substrate NAD(+) at ART2.2. Two of the bacterial enzymes are structurally more closely related to ART2.2 while the others are more closely related to the eukaryotic poly(ADP-ribosyl)polymerase. This splits the ADP-ribosyl transferases into two distinct subfamilies. A special feature of ART2.2 is its long N-terminal extension and two disulfide bridges that are far away from the active center. They stabilize the protein against denaturation and presumably also against shearing forces parallel with the membrane where ART2.2 is anchored.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Superposition of the eukaryotic ART2.2 on one hand (black and gray) with the bacterial VIP2C (yellow, atom colors),[25] the bacterial exotoxin A (green), [37] the diphtheria toxin (blue), [38] and chicken polymerase (red) [6] on the other. The superpositions are on the basis of the C^a atoms of the depicted structurally conserved 25 residues at the active center, which we have named four-stranded b-core (Figure 1(a)). They comprise members of both subfamilies. The strictly conserved glutamate is shown. The residue numbers are from ART2.2. The superposition relates the ligands BNA of ART2.2, NAD^+ of VIP2C, the NAD^+ analogue of ETA, NAD^+ of diphtheria toxin and the nicotinamide analogue of the polymerase to each other.
Figure 5.
Figure 5. Sketch of rat ecto-ART2.2 as fastened by a GPI-anchor to the membrane. The N and C-terminal polypeptide segments, which are not present in the closest bacterial homologues VIP2C and exotoxin C3, are drawn as stippled lines. The depicted disulfide bridge and the N and C-terminal additions with respect to the bacterial toxins are probably designed to resist shear forces likely to occur along the membrane in rough extracellular environments. Note that the enzyme is viewed essentially upside down when compared to Figure 1, Figure 4, Figure 6 and Figure 7.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 322, 687-696) copyright 2002.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21175663 N.M.Burton, and G.Daniels (2011).
Structural modelling of red cell surface proteins.
  Vox Sang, 100, 129-139.  
  19255877 N.Schwarz, R.Fliegert, S.Adriouch, M.Seman, A.H.Guse, F.Haag, and F.Koch-Nolte (2009).
Activation of the P2X7 ion channel by soluble and covalently bound ligands.
  Purinergic Signal, 5, 139-149.  
  19234763 S.Adriouch, F.Scheuplein, R.Bähring, M.Seman, O.Boyer, F.Koch-Nolte, and F.Haag (2009).
Characterisation of the R276A gain-of-function mutation in the ectodomain of murine P2X7.
  Purinergic Signal, 5, 151-161.  
18490658 H.Tsuge, M.Nagahama, M.Oda, S.Iwamoto, H.Utsunomiya, V.E.Marquez, N.Katunuma, M.Nishizawa, and J.Sakurai (2008).
Structural basis of actin recognition and arginine ADP-ribosylation by Clostridium perfringens iota-toxin.
  Proc Natl Acad Sci U S A, 105, 7399-7404.
PDB code: 3buz
18349144 J.Baysarowich, K.Koteva, D.W.Hughes, L.Ejim, E.Griffiths, K.Zhang, M.Junop, and G.D.Wright (2008).
Rifamycin antibiotic resistance by ADP-ribosylation: Structure and diversity of Arr.
  Proc Natl Acad Sci U S A, 105, 4886-4891.
PDB code: 2hw2
17655578 C.Westhoff, S.Vege, K.Yazdanbakhsh, D.Wylie, M.Razib, K.Hue-Roye, G.Halverson, S.Read, E.Whiteoak, P.Nickle, J.Maurer, D.Kavitsky, S.Nance, and M.E.Reid (2007).
A DOB allele encoding an amino acid substitution (Phe62Ser) resulting in a Dombrock null phenotype.
  Transfusion, 47, 1356-1362.  
16931513 A.R.Morrison, J.Moss, L.A.Stevens, J.E.Evans, C.Farrell, E.Merithew, D.G.Lambright, D.L.Greiner, J.P.Mordes, A.A.Rossini, and R.Bortell (2006).
ART2, a T cell surface mono-ADP-ribosyltransferase, generates extracellular poly(ADP-ribose).
  J Biol Chem, 281, 33363-33372.  
17015823 C.Mueller-Dieckmann, S.Kernstock, M.Lisurek, J.P.von Kries, F.Haag, M.S.Weiss, and F.Koch-Nolte (2006).
The structure of human ADP-ribosylhydrolase 3 (ARH3) provides insights into the reversibility of protein ADP-ribosylation.
  Proc Natl Acad Sci U S A, 103, 15026-15031.
PDB codes: 2foz 2fp0
16956368 K.P.Holbourn, C.C.Shone, and K.R.Acharya (2006).
A family of killer toxins. Exploring the mechanism of ADP-ribosylating toxins.
  FEBS J, 273, 4579-4593.  
  16511307 S.Kernstock, F.Koch-Nolte, J.Mueller-Dieckmann, M.S.Weiss, and C.Mueller-Dieckmann (2006).
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of human ARH3, the first eukaryotic protein-ADP-ribosylhydrolase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 224-227.  
16156779 M.Di Girolamo, N.Dani, A.Stilla, and D.Corda (2005).
Physiological relevance of the endogenous mono(ADP-ribosyl)ation of cellular proteins.
  FEBS J, 272, 4565-4575.  
16195877 S.Rothenburg, F.Haag, F.Koch-Nolte, C.Carter, M.Graham, and G.W.Butcher (2005).
Characterization of multiple alleles of the T-cell differentiation marker ART2 (RT6) in inbred and wild rats.
  Immunogenetics, 57, 739-749.  
12721285 C.Bourgeois, I.Okazaki, E.Cavanaugh, M.Nightingale, and J.Moss (2003).
Identification of regulatory domains in ADP-ribosyltransferase-1 that determine transferase and NAD glycohydrolase activities.
  J Biol Chem, 278, 26351-26355.  
14563321 M.Seman, S.Adriouch, F.Scheuplein, C.Krebs, D.Freese, G.Glowacki, P.Deterre, F.Haag, and F.Koch-Nolte (2003).
NAD-induced T cell death: ADP-ribosylation of cell surface proteins by ART2 activates the cytolytic P2X7 purinoceptor.
  Immunity, 19, 571-582.  
14604445 S.Washietl, and F.Eisenhaber (2003).
Reannotation of the CELO genome characterizes a set of previously unassigned open reading frames and points to novel modes of host interaction in avian adenoviruses.
  BMC Bioinformatics, 4, 55.  
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 code is shown on the right.