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(-) Description

Title :  CRYSTAL STRUCTURE OF A DIMETAL PHOSPHATASE FROM DANIO RERIO LOC 393393
 
Authors :  E. Bitto, G. E. Wesenberg, G. N. Phillips Jr. , J. G. Mccoy, C. A. Bingman For Eukaryotic Structural Genomics (Cesg)
Date :  17 Nov 06  (Deposition) - 12 Dec 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Dinuclear Metal Center Phosphatase, Metalloprotein, Metallophosphoesterase, Protein Structure Initiative, Center For Eukaryotic Structural Genomics, Cesg, Psi-2, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Bitto, G. E. Wesenberg, G. N. Phillips Jr. , J. G. Mccoy, C. A. Bingma
Crystal Structure Of A Dimetal Phosphatase From Danio Rerio Loc 393393
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE DIMETAL PHOSPHATASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP 16K
    Expression System Strain: BL834 P(RARE2)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DR.12833, LOC 393393
    Organism Common: ZEBRAFISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1EOH1Ligand/IonETHANOL
2MSE3Mod. Amino AcidSELENOMETHIONINE
3PO41Ligand/IonPHOSPHATE ION
4ZN4Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:13 , GLN A:15 , ASP A:60 , HIS A:267 , ZN A:402 , PO4 A:501 , HOH A:844BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREASP A:60 , ASN A:96 , HIS A:228 , HIS A:265 , ZN A:401 , PO4 A:501 , HOH A:844BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWAREHIS A:174 , HOH A:694BINDING SITE FOR RESIDUE ZN A 403
4AC4SOFTWAREHIS A:166 , ILE A:170 , HOH A:628 , HOH A:646BINDING SITE FOR RESIDUE ZN A 404
5AC5SOFTWAREGLN A:15 , ARG A:31 , ASP A:60 , ASN A:96 , HIS A:97 , HIS A:265 , HIS A:267 , ZN A:401 , ZN A:402 , HOH A:690 , HOH A:844BINDING SITE FOR RESIDUE PO4 A 501
6AC6SOFTWAREARG A:51 , VAL A:52 , CYS A:86 , VAL A:88 , HOH A:856BINDING SITE FOR RESIDUE EOH A 502

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:234 -A:272

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2NXF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NXF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2NXF)

(-) Exons   (0, 0)

(no "Exon" information available for 2NXF)

(-) 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:314
 aligned with ADPRM_DANRE | Q7T291 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:320
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322
          ADPRM_DANRE     3 DPVFTFGLIADVQYADIEDGENYLRTRRRYYRGSADLLRDAVLQWRRERVQCVVQLGDIIDGHNRRRDASDRALDTVMAELDACSVDVHHVWGNHEFYNFSRPSLLSSRLNSAQRTGTDTGSDLIGDDIYAYEFSPAPNFRFVLLDAYDLSVIGREEESEKHTHSWRILTQHNHNLQDLNLPPVSVGLEQRFVKFNGGFSEQQLQWLDAVLTLSDHKQERVLIFSHLPVHPCAADPICLAWNHEAVLSVLRSHQSVLCFIAGHDHDGGRCTDSSGAQHITLEGVIETPPHSHAFATAYLYEDRMVMKGRGRVEDLTITYS 322
               SCOP domains d2nxfa1 A:3-322 Uncharacterized C17orf48 homolog zgc:64213                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2nxfA01 A:3-314  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                                                                     -------- CATH domains
               Pfam domains -----Metallophos_2-2nxfA01 A:8-305                                                                                                                                                                                                                                                                             ----------------- Pfam domains
         Sec.struct. author ...eeeeee..........ee......ee..hhhhhhhhhhhhhhhhh...eeee......hhhhhh.hhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhh.......------.ee.hhhh...eeeeee..eeeee..............hhhhhhhhhhhhhhh.............hhhhhh.......hhhhhhhhhhhhhhhhhhh.eeeeee.........hhhhh..hhhhhhhhhhh...eeeeee......eeee.....eeee..hhhhh.....eeeeeee...eeeeeeee....eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nxf A   3 DPVFTFGLIADVQYADIEDGENYLRTRRRYYRGSADLLRDAVLQWRRERVQCVVQLGDIIDGHNRRRDASDRALDTVmAELDACSVDVHHVWGNHEFYNFSRPSLLSSRLNSAQ------GSDLIGDDIYAYEFSPAPNFRFVLLDAYDLSVIGREEESEKHTHSWRILTQHNHNLQDLNLPPVSVGLEQRFVKFNGGFSEQQLQWLDAVLTLSDHKQERVLIFSHLPVHPCAADPICLAWNHEAVLSVLRSHQSVLCFIAGHDHDGGRCTDSSGAQHITLEGVIETPPHSHAFATAYLYEDRmVmKGRGRVEDLTITYS 322
                                    12        22        32        42        52        62        72       |82        92       102       112   |     -|      132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302   | | 312       322
                                                                                                        80-MSE                             116    123                                                                                                                                                                                    306-MSE            
                                                                                                                                                                                                                                                                                                                                           308-MSE
   Legend:   → Mismatch (orange background)
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  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: Calcineurin (56)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ADPRM_DANRE | Q7T291)
molecular function
    GO:0008663    2',3'-cyclic-nucleotide 2'-phosphodiesterase activity    Catalysis of the reaction: nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 3'-phosphate.
    GO:0047631    ADP-ribose diphosphatase activity    Catalysis of the reaction: ADP-ribose + H2O = AMP + D-ribose 5-phosphate.
    GO:0047734    CDP-glycerol diphosphatase activity    Catalysis of the reaction: CDP-glycerol + H(2)O = sn-glycerol 3-phosphate + CMP + 2 H(+).
    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:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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