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(-) Description

Title :  RAT NTPDASE2 IN COMPLEX WITH CA AMPNP
 
Authors :  M. Zebisch, P. Schaefer, P. Lauble, N. Straeter
Date :  03 Jun 13  (Deposition) - 17 Jul 13  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Apyrase, Atpase, Adpase, Purinergic Signalling, Domain Rotation, Transition State, Ntpdase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Zebisch, M. Krauss, P. Schaefer, P. Lauble, N. Straeter
Crystallographic Snapshots Along The Reaction Pathway Of Nucleoside Triphosphate Diphosphohydrolases
Structure V. 21 1460 2013
PubMed-ID: 23830739  |  Reference-DOI: 10.1016/J.STR.2013.05.016

(-) 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: 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  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1AU11Ligand/Ion5'-O-[(R)-HYDROXY(PHOSPHONOAMINO)PHOSPHORYL]ADENOSINE
2CA1Ligand/IonCALCIUM ION
3GOL5Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:47 , SER A:48 , SER A:49 , HIS A:50 , THR A:122 , ALA A:123 , GLU A:165 , GLY A:203 , GLY A:204 , ALA A:205 , SER A:206 , ARG A:245 , ASP A:246 , TYR A:350 , ARG A:394 , TYR A:398 , CA A:1463 , HOH A:2046 , HOH A:2069 , HOH A:2070 , HOH A:2121 , HOH A:2124BINDING SITE FOR RESIDUE AU1 A1462
2AC2SOFTWAREAU1 A:1462 , HOH A:2003 , HOH A:2005 , HOH A:2070 , HOH A:2101BINDING SITE FOR RESIDUE CA A1463
3AC3SOFTWAREARG A:245 , ASP A:246 , ARG A:394 , ASP A:397 , GOL A:1465 , HOH A:2123 , HOH A:2188BINDING SITE FOR RESIDUE GOL A1464
4AC4SOFTWARELEU A:249 , LEU A:253 , TRP A:266 , ASP A:397 , GOL A:1464 , HOH A:2123 , HOH A:2126BINDING SITE FOR RESIDUE GOL A1465
5AC5SOFTWAREPHE A:168 , LEU A:228 , ASN A:443 , HOH A:2113 , HOH A:2183 , HOH A:2189BINDING SITE FOR RESIDUE GOL A1466
6AC6SOFTWAREARG A:251 , CYS A:284 , GLN A:288 , LEU A:317 , HOH A:2128BINDING SITE FOR RESIDUE GOL A1467
7AC7SOFTWARELEU A:241 , CYS A:242 , HOH A:2141BINDING SITE FOR RESIDUE GOL A1468

(-) 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 4BR0)

(-) 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 4BR0)

(-) 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:420
 aligned with ENTP2_RAT | O35795 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:427
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       
            ENTP2_RAT    36 PALKYGIVLDAGSSHTSMFVYKWPADKENDTGIVGQHSSCDVQGGGISSYANDPSKAGQSLVRCLEQALRDVPRDRHASTPLYLGATAGMRPFNLTSPEATARVLEAVTQTLTQYPFDFRGARILSGQDEGVFGWVTANYLLENFIKYGWVGRWIRPRKGTLGAMDLGGASTQITFETTSPSEDPGNEVHLRLYGQHYRVYTHSFLCYGRDQILLRLLASALQIHRFHPCWPKGYSTQVLLQEVYQSPCTMGQRPRAFNGSAIVSLSGTSNATLCRDLVSRLFNISSCPFSQCSFNGVFQPPVAGNFIAFSAFYYTVDFLTTVMGLPVGTLKQLEEATEITCNQTWTELQARVPGQKTRLADYCAVAMFIHQLLSRGYHFDERSFREVVFQKKAADTAVGWALGYMLNLTNLIPADLPGLRKGTHFS 462
               SCOP domains d4br0a1 A:36-178 automated matches                                                                                                             d4br0a2 A:179-462 automated matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....eeeeeeeee.hhh......eeeeeee....hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhh......ee..ee........eeeee...eeeeeee......hhh.eeeeee..eeeeeeeeeee..hhhhhhhhhhhhhhhhh..........eeeeehhhhhh.......-------..eeeee...hhhhhhhhhhh.........................eeeeehhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...hhhhhh.eee..ee..ee..hhhhhhhhhh......hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------GDA1_CD39_NTPASE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4br0 A  36 PALKYGIVLDAGSSHTSMFVYKWPADKENDTGIVGQHSSCDVQGGGISSYANDPSKAGQSLVRCLEQALRDVPRDRHASTPLYLGATAGMRLLNLTSPEATARVLEAVTQTLTQYPFDFRGARILSGQDEGVFGWVTANYLLENFIKYGWVGRWIRPRKGTLGAMDLGGASTQITFETTSPSEDPGNEVHLRLYGQHYRVYTHSFLCYGRDQILLRLLASALQIHRFHPCWPKGYSTQVLLQEVYQSPCTMGQ-------SAIVSLSGTSNATLCRDLVSRLFNISSCPFSQCSFNGVFQPPVAGNFIAFSAFYYTVDFLTTVMGLPVGTLKQLEEATEITCNQTWTELQARVPGQKTRLADYCAVAMFIHQLLSRGYHFDERSFREVVFQKKAADTAVGWALGYMLNLTNLIPADLPGLRKGTHFS 462
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285  |      -|      305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       
                                                                                                                                                                                                                                                                                      288     296
   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 4BR0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BR0)

(-) 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 4br2 4br5 4cd1 4cd3

(-) Related Entries Specified in the PDB File

3cj1 STRUCTURE OF RATTUS NORVEGICUS NTPDASE2
3cj7 STRUCTURE OF RATTUS NORVEGICUS NTPDASE2 IN COMPLEX WITH AMP
3cj9 STRUCTURE OF RATTUS NORVEGICUS NTPDASE2 IN COMPLEX WITH CALCIUM, AMP AND PHOSPHATE
3cja STRUCTURE OF RATTUS NORVEGICUS NTPDASE2 IN COMPLEX WITH CALCIUM AND AMPPNP
4bqz RAT NTPDASE2 IN COMPLEX WITH MG GMPPNP
4br2 RAT NTPDASE2 IN COMPLEX WITH CA UMPPNP
4br4 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM I, OPEN, APO
4br5 RNNTPDASE2 IN COMPLEX WITH ZNAMPPNP
4br7 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM I, OPEN, APO
4br9 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, APO
4bra LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, MG AMPPNP COMPLEX
4brc LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, MG AMPNP COMPLEX
4brd LEGIONELLA PNEUMOPHILA NTPDASE1 Q193E CRYSTAL FORM II, CLOSED, MG AMPPNP COMPLEX
4bre LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH TRANSITION STATE MIMIC ADENOSINE 5' PHOSPHOVANADATE
4brf LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH A DISTORTED ORTHOMOLYBDATE ION AND AMP
4brg LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH MG GMPPNP
4brh LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH MG AND THIAMINE PHOSPHOVANADATE
4bri LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH MG UMPPNP
4brk LEGIONELLA PNEUMOPHILA NTPDASE1 N302Y VARIANT CRYSTAL FORM III (CLOSED) IN COMPLEX WITH MG UMPPNP
4brl LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM III (CLOSED) IN COMPLEX WITH TRANSITION STATE MIMI GUANOSINE 5'- PHOSPHOVANADATE
4brm SULFUR SAD PHASING OF THE LEGIONELLA PNEUMOPHILA NTPDASE1 - CRYSTAL FORM III (CLOSED) IN COMPLEX WITH SULFATE
4brn LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM III (CLOSED) IN COMPLEX WITH MG AMP
4bro LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM IV (PART- OPEN)
4brp LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM V (PART- OPEN)
4brq LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, IN COMPLEX WITH TWO PHOSPHATES BOUND TO ACTIVE SITE MG AND PRODUCT AMP