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(-) Description

Title :  SOLUTION STRUCTURE OF THE NUDIX ENZYME DIADENOSINE TETRAPHOSPHATE HYDROLASE FROM LUPINUS ANGUSTIFOLIUS COMPLEXED WITH ATP
 
Authors :  J. I. Fletcher, J. D. Swarbrick, D. Maksel, K. R. Gayler, P. R. Gooley
Date :  12 Jul 01  (Deposition) - 27 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (30x)
Keywords :  Alpha-Beta-Alpha Sandwich, Enzyme-Substrate Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. I. Fletcher, J. D. Swarbrick, D. Maksel, K. R. Gayler, P. R. Gooley
The Structure Of Ap(4)A Hydrolase Complexed With Atp-Mgf(X) Reveals The Basis Of Substrate Binding.
Structure V. 10 205 2002
PubMed-ID: 11839306  |  Reference-DOI: 10.1016/S0969-2126(02)00696-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIADENOSINE 5',5'''-P1,P4-TETRAPHOSPHATE HYDROLASE
    Chains: A
    EC Number: 3.6.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX-6P-3
    Expression System Strain: BL-21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: NARROW-LEAVED BLUE LUPINE
    Organism Scientific: LUPINUS ANGUSTIFOLIUS
    Organism Taxid: 3871

 Structural Features

(-) Chains, Units

  
NMR Structure (30x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:16 , ARG A:33 , GLN A:41 , GLN A:44 , TYR A:82 , PHE A:84 , VAL A:88 , LYS A:91 , TRP A:96 , GLN A:103 , VAL A:147 , PHE A:149 , LYS A:150BINDING SITE FOR RESIDUE ATP A 166

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JKN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JKN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JKN)

(-) Exons   (0, 0)

(no "Exon" information available for 1JKN)

(-) Sequences/Alignments

NMR Structure
   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:165
 aligned with O04841_LUPAN | O04841 from UniProtKB/TrEMBL  Length:199

    Alignment length:191
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198 
         O04841_LUPAN     9 SPPTNFHFRKYPSKFLKFSSLSLAFRYCHSSMDSPPEGYRRNVGICLMNNDKKIFAASRLDIPDAWQMPQGGIDEGEDPRNAAIRELREETGVTSAEVIAEVPYWLTYDFPPKVREKLNIQWGSDWKGQAQKWFLFKFTGQDQEINLLGDGSEKPEFGEWSWVTPEQLIDLTVEFKKPVYKEVLSVFAPHL 199
               SCOP domains d1                          jkna_ A: Diadenosine tetraphosphate hydrolase (Ap4A hydrolase)                                                                                                      SCOP domains
               CATH domains 1j                          knA00 A:1-165 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                          CATH domains
               Pfam domains --------------------------------------NUDIX-1jknA01 A:13-160                                                                                                                              ----- Pfam domains
         Sec.struct. author ..--------------------------..........eeeeeeeeee.....eeeeee......ee..ee......hhhhhhhhhhhhhh....eeeeee....eeee.hhhhhhhhhhhh.....eeee..eeeee..................eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jkn A   1 GP--------------------------LGSMDSPPEGYRRNVGICLMNNDKKIFAASRLDIPDAWQMPQGGIDEGEDPRNAAIRELREETGVTSAEVIAEVPYWLTYDFPPKVREKLNIQWGSDWKGQAQKWFLFKFTGQDQEINLLGDGSEKPEFGEWSWVTPEQLIDLTVEFKKPVYKEVLSVFAPHL 165
                             |       -         -        |4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164 
                             2                          3
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  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)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: NUDIX (85)

(-) Gene Ontology  (4, 4)

NMR Structure(hide GO term definitions)
Chain A   (O04841_LUPAN | O04841)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004081    bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity    Catalysis of the reaction: P(1),P(4)-bis(5'-nucleosyl)tetraphosphate + H2O = NTP + NMP. Acts on bis(5'-guanosyl)-, bis(5'-xanthosyl)-, bis(5'-adenosyl)- and bis(5'-uridyl)-tetraphosphate.
    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: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.

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 Related Entries

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

UniProtKB/TrEMBL
        O04841_LUPAN | O04841: 1f3y

(-) Related Entries Specified in the PDB File

1f3y 1F3Y CONTAINS THE SAME PROTEIN IN THE FREE FORM