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(-) Description

Title :  RNNTPDASE2 IN COMPLEX WITH PSB-071
 
Authors :  M. Zebisch, P. Schaefer, N. Straeter
Date :  29 Oct 13  (Deposition) - 12 Feb 14  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Apyrase, Atpase, Purinergic Signalling, Cd39, Drug Design, Inhibitor, Ntpdase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Zebisch, Y. Baqi, P. Schafer, C. E. Muller, N. Strater
Crystal Structure Of Ntpdase2 In Complex With The Sulfoanthraquinone Inhibitor Psb-071.
J. Struct. Biol. V. 185 336 2014
PubMed-ID: 24462745  |  Reference-DOI: 10.1016/J.JSB.2014.01.005

(-) Compounds

Molecule 1 - ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 2
    Chains: A
    EC Number: 3.6.1.-, 3.6.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: ECTODOMAIN, RESIDUES 28-462
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: NTPDASE 2, CD39 ANTIGEN-LIKE 1, ECTO-ATP DIPHOSPHOHYDROLASE 2, ECTO-ATPDASE 2, ECTO-ATPASE 2, NTPDASE2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
18E92Ligand/Ion1-AMINO-4-(3-METHYLPHENYL)AMINO-9,10-DIOXO-9,10-DIHYDROANTHRACENE-2-SULFONATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:50 , ARG A:245 , LEU A:249 , LYS A:392 , THR A:393 , ARG A:394 , TYR A:398 , 8E9 A:1453BINDING SITE FOR RESIDUE 8E9 A1452
2AC2SOFTWARESER A:52 , ASP A:76 , ARG A:245 , SER A:346 , TYR A:350 , TYR A:398 , 8E9 A:1452BINDING SITE FOR RESIDUE 8E9 A1453

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:75 -A:99
2A:242 -A:284
3A:265 -A:310
4A:323 -A:328
5A:377 -A:399

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:191 -Pro A:192

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CD1)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GDA1_CD39_NTPASEPS01238 GDA1/CD39 family of nucleoside phosphatases signature.ENTP2_RAT160-175  1A:160-175

(-) Exons   (0, 0)

(no "Exon" information available for 4CD1)

(-) 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:406
 aligned with ENTP2_RAT | O35795 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:414
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447    
            ENTP2_RAT    38 LKYGIVLDAGSSHTSMFVYKWPADKENDTGIVGQHSSCDVQGGGISSYANDPSKAGQSLVRCLEQALRDVPRDRHASTPLYLGATAGMRPFNLTSPEATARVLEAVTQTLTQYPFDFRGARILSGQDEGVFGWVTANYLLENFIKYGWVGRWIRPRKGTLGAMDLGGASTQITFETTSPSEDPGNEVHLRLYGQHYRVYTHSFLCYGRDQILLRLLASALQIHRFHPCWPKGYSTQVLLQEVYQSPCTMGQRPRAFNGSAIVSLSGTSNATLCRDLVSRLFNISSCPFSQCSFNGVFQPPVAGNFIAFSAFYYTVDFLTTVMGLPVGTLKQLEEATEITCNQTWTELQARVPGQKTRLADYCAVAMFIHQLLSRGYHFDERSFREVVFQKKAADTAVGWALGYMLNLTNLIPAD 451
               SCOP domains d4cd1a1 A:38-178 automated matches                                                                                                           d4cd1a2 A:179-451 automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee....eeeeeeeehhhhh......eeeeeee....hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhhh......ee..ee........eeeee...eeeeeee......hhh.eeeeee..eeeeeeeeeee..hhhhhhhhhhhhhhhhh..........eeeeehhhhhhhhhhh..--------.eeeee...hhhhhhhhhhh.........................eeeeehhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh....hhhhhh.eee..ee..ee..hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------GDA1_CD39_NTPASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4cd1 A  38 LKYGIVLDAGSSHTSMFVYKWPADKENDTGIVGQHSSCDVQGGGISSYANDPSKAGQSLVRCLEQALRDVPRDRHASTPLYLGATAGMRLLNLTSPEATARVLEAVTQTLTQYPFDFRGARILSGQDEGVFGWVTANYLLENFIKYGWVGRWIRPRKGTLGAMDLGGASTQITFETTSPSEDPGNEVHLRLYGQHYRVYTHSFLCYGRDQILLRLLASALQIHRFHPCWPKGYSTQVLLQEVYQSPCTMGQ--------AIVSLSGTSNATLCRDLVSRLFNISSCPFSQCSFNGVFQPPVAGNFIAFSAFYYTVDFLTTVMGLPVGTLKQLEEATEITCNQTWTELQARVPGQKTRLADYCAVAMFIHQLLSRGYHFDERSFREVVFQKKAADTAVGWALGYMLNLTNLIPAD 451
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287|      297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447    
                                                                                                                                                                                                                                                                                    288      297
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CD1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CD1)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ENTP2_RAT | O35795)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0043262    adenosine-diphosphatase activity    Catalysis of the reaction: ADP + H2O = AMP + phosphate.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0035457    cellular response to interferon-alpha    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-alpha stimulus. Interferon-alpha is a type I interferon.
    GO:0071354    cellular response to interleukin-6    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-6 stimulus.
    GO:0071222    cellular response to lipopolysaccharide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0071356    cellular response to tumor necrosis factor    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0010996    response to auditory stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an auditory stimulus.
cellular component
    GO:0044297    cell body    The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
    GO:0031253    cell projection membrane    The portion of the plasma membrane surrounding a plasma membrane bounded cell surface projection.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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
        ENTP2_RAT | O35795: 3cj1 3cj7 3cj9 3cja 4bqz 4br0 4br2 4br5 4cd3

(-) Related Entries Specified in the PDB File

4cd3 RNNTPDASE2 X4 VARIANT IN COMPLEX WITH PSB-071