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(-) Description

Title :  CRYSTAL STRUCTURE OF THE EUKARYOTIC MONO-ADP-RIBOSYLTRANSFERASE ART2.2 MUTANT E189I IN COMPLEX WITH NAD
 
Authors :  H. Ritter, F. Koch-Nolte, V. E. Marquez, G. E. Schulz
Date :  24 Apr 03  (Deposition) - 28 Aug 03  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Adp-Ribosyltransferase, Immuno-Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Ritter, F. Koch-Nolte, V. E. Marquez, G. E. Schulz
Substrate Binding And Catalysis Of Ecto-Adp-Ribosyltransferase 2. 2 From Rat
Biochemistry V. 42 10155 2003
PubMed-ID: 12939142  |  Reference-DOI: 10.1021/BI034625W

(-) Compounds

Molecule 1 - T-CELL ECTO-ADP-RIBOSYLTRANSFERASE 2
    Chains: A
    EC Number: 2.4.2.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PASK60
    Expression System Strain: NM522
    Expression System Taxid: 562
    Fragment: RESIDUES 21-246
    Mutation: YES
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:5 , LYS A:65 , VAL A:84 , ASN A:87 , ARG A:91 , ARG A:126 , GLY A:127 , THR A:130 , PHE A:132 , GLN A:144 , SER A:147 , PHE A:160 , GLN A:187 , ILE A:189 , HOH A:2056 , HOH A:2057 , HOH A:2058 , HOH A:2065 , HOH A:2068 , HOH A:2069 , HOH A:2099 , HOH A:2120 , HOH A:2126 , HOH A:2149 , HOH A:2150 , HOH A:2151 , HOH A:2152 , HOH A:2153 , HOH A:2154BINDING SITE FOR RESIDUE NAD A1227

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:21 -A:223
2A:121 -A:173

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:184 -Pro A:185

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OG3)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARTPS01291 NAD:arginine ADP-ribosyltransferases signature.NAR2B_RAT120-132  1A:100-112

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000266441ENSRNOE00000373063chr1:159058780-15905870774NAR2B_RAT1-17170--
1.3ENSRNOT000000266443ENSRNOE00000444749chr1:159058239-159057546694NAR2B_RAT18-2492321A:4-226223
1.4ENSRNOT000000266444ENSRNOE00000425759chr1:159055875-159055461415NAR2B_RAT249-275270--

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:223
 aligned with NAR2B_RAT | P20974 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:223
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   
            NAR2B_RAT    24 PLMLDTAPNAFDDQYEGCVNKMEEKAPLLLQEDFNMNAKLKVAWEEAKKRWNNIKPSRSYPKGFNDFHGTALVAYTGSIAVDFNRAVREFKENPGQFHYKAFHYYLTRALQLLSNGDCHSVYRGTKTRFHYTGAGSVRFGQFTSSSLSKKVAQSQEFFSDHGTLFIIKTCLGVYIKEFSFRPDQEEVLIPGYEVYQKVRTQGYNEIFLDSPKRKKSNYNCLYS 246
               SCOP domains d1og3a_ A: Eukaryotic mono-ADP-ribosyltransferase ART2.2                                                                                                                                                                        SCOP domains
               CATH domains 1og3A00 A:4-226 Toxin ADP-ribosyltransferase; Chain A, domain 1                                                                                                                                                                 CATH domains
               Pfam domains ---ART-1og3A01 A:7-219                                                                                                                                                                                                  ------- Pfam domains
         Sec.struct. author .eee..............hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh.hhhhhhhhhhhh..........hhhhhhhhhhhhhh.....eeeeeee..eee......ee....eeeee.hhhhh.........eeeeeee...ee...........eeee...eeeeeeeee...eeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ART          ------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.3  PDB: A:4-226 UniProt: 18-249 [INCOMPLETE]                                                                                                                                                                             Transcript 1
                 1og3 A   4 PLMLDTAPNAFDDQYEGCVNKMEEKAPLLLQEDFNMNAKLKVAWEEAKKRWNNIKPSRSYPKGFNDFHGTALVAYTGSIAVDFNRAVREFKENPGQFHYKAFHYYLTRALQLLSNGDCHSVYRGTKTRFHYTGAGSVRFGQFTSSSLSKKVAQSQEFFSDHGTLFIIKTCLGVYIKEFSFRPDQEIVLIPGYEVYQKVRTQGYNEIFLDSPKRKKSNYNCLYS 226
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: ADP-ribosyl (56)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NAR2B_RAT | P20974)
molecular function
    GO:0003956    NAD(P)+-protein-arginine ADP-ribosyltransferase activity    Catalysis of the reaction: NAD(P)+ + L-arginine = nicotinamide + N2-(ADP-D-ribosyl)-L-arginine.
    GO:0003953    NAD+ nucleosidase activity    Catalysis of the reaction: NAD+ + H2O = nicotinamide + ADP-ribose.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0019677    NAD catabolic process    The chemical reactions and pathways resulting in the breakdown of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; catabolism may be of either the oxidized form, NAD, or the reduced form, NADH.
    GO:0006471    protein ADP-ribosylation    The transfer, from NAD, of ADP-ribose to protein amino acids.
cellular component
    GO:0031225    anchored component of membrane    The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0046658    anchored component of plasma membrane    The component of the plasma membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group, that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NAR2B_RAT | P20974: 1gxy 1gxz 1gy0 1og1 1og4

(-) Related Entries Specified in the PDB File

1gxy CRYSTAL STRUCTURE OF THE EUCARYOTIC MONO-ADP -RIBOSYLTRANSFERASE ART2.2
1gxz CRYSTAL STRUCTURE OF THE EUCARYOTIC MONO-ADP -RIBOSYLTRANSFERASE ART2.2
1gy0 CRYSTAL STRUCTURE OF THE EUCARYOTIC MONO-ADP -RIBOSYLTRANSFERASE ART2.2
1og1 CRYSTAL STRUCTURE OF THE EUCARYOTIC MONO-ADP -RIBOSYLTRANSFERASE ART2.2 IN COMPLEX WITH TAD
1og4 CRYSTAL STRUCTURE OF THE EUCARYOTIC MONO-ADP -RIBOSYLTRANSFERASE ART2.2 MUTANT E189A IN COMPLEX WITH NADH