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(-) Description

Title :  STRUCTURE OF THE NUDIX ENZYME AP4A HYDROLASE FROM HOMO SAPIENS (E63A MUTANT) IN COMPLEX WITH ATP
 
Authors :  J. D. Swarbrick, S. Buyya, D. Gunawardana, K. R. Gayler, A. G. Mclennan, P. R. Gooley
Date :  18 Oct 04  (Deposition) - 21 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (25x)
Keywords :  Nudix Enzyme, Human Ap4A Atp Hydrolase, Nmr, Alpha-Beta (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. D. Swarbrick, S. Buyya, D. Gunawardana, K. R. Gayler, A. G. Mclennan, P. R. Gooley
Structure And Substrate-Binding Mechanism Of Human Ap4A Hydrolase
J. Biol. Chem. V. 280 8471 2005
PubMed-ID: 15596429  |  Reference-DOI: 10.1074/JBC.M412318200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BIS(5'-NUCLEOSYL)-TETRAPHOSPHATASE
    ChainsA
    EC Number3.6.1.17
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-6-P3
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDIADENOSINE 5',5'''-P1,P4-TETRAPHOSPHATE ASYMMETRICAL HYDROLASE, DIADENOSINE TETRAPHOSPHATASE, AP4A HYDROLASE, AP4AASE

 Structural Features

(-) Chains, Units

  
NMR Structure (25x)

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
1AC1SOFTWAREHIS A:42 , TYR A:87 , ALA A:89 , PHE A:133 , GLU A:135BINDING SITE FOR RESIDUE ATP A 154

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIXPS51462 Nudix hydrolase domain profile.AP4A_HUMAN1-139  1A:6-144
2NUDIX_BOXPS00893 Nudix box signature.AP4A_HUMAN43-64  1A:48-69

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003791581ENSE00001357806chr9:34329504-3432959794AP4A_HUMAN-00--
1.3aENST000003791583aENSE00001479918chr9:34336226-34336339114AP4A_HUMAN-00--
1.4bENST000003791584bENSE00001357794chr9:34338711-34338845135AP4A_HUMAN-00--
1.5aENST000003791585aENSE00001089099chr9:34339022-34339164143AP4A_HUMAN1-43431A:6-4843
1.6cENST000003791586cENSE00001479910chr9:34343122-34343709588AP4A_HUMAN43-1471051A:48-152105

(-) 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:153
 aligned with AP4A_HUMAN | P50583 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:153
                                 1                                                                                                                                               147 
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145 | 
           AP4A_HUMAN     - -----MALRACGLIIFRRCLIPKVDNNAIEFLLLQASDGIHHWTPPKGHVEPGEDDLETALRETQEEAGIEAGQLTIIEGFKRELNYVARNKPKTVIYWLAEVKDYDVEIRLSHEHQAYRWLGLEEACQLAQFKEMKAALQEGHQFLCSIEA-   -
               SCOP domains d1xsca_ A: Diadenosine tetraphosphate hydrolase (Ap4A hydrolase)                                                                                          SCOP domains
               CATH domains 1xscA00 A:1-153 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                              CATH domains
               Pfam domains ------NUDIX-1xscA01 A:7-142                                                                                                                   ----------- Pfam domains
         Sec.struct. author .......eeeeeeee...............eeeeee......ee..ee......hhhhhhhhhhhhhh..hhhhh.......eeeeee....eeeeeeeee..............eeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----NUDIX  PDB: A:6-144 UniProt: 1-139                                                                                                         --------- PROSITE (1)
                PROSITE (2) -----------------------------------------------NUDIX_BOX  PDB: A:48-6------------------------------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) -----Exon 1.5a  PDB: A:6-48 UniProt: 1-43       --------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.6c  PDB: A:48-152 UniProt: 43-147                                                                 - Transcript 1 (2)
                 1xsc A   1 GPLGSMALRACGLIIFRRCLIPKVDNNAIEFLLLQASDGIHHWTPPKGHVEPGEDDLETALRATQEEAGIEAGQLTIIEGFKRELNYVARNKPKTVIYWLAEVKDYDVEIRLSHEHQAYRWLGLEEACQLAQFKEMKAALQEGHQFLCSIEAL 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   

   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)

NMR Structure

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: NUDIX (85)

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (AP4A_HUMAN | P50583)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    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:0008803    bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity    Catalysis of the reaction: P(1),P(4)-bis(5'-adenosyl) tetraphosphate + H(2)O = 2 ADP + 2 H(+).
    GO:0008796    bis(5'-nucleosyl)-tetraphosphatase activity    Catalysis of the hydrolysis of P(1),P(4)-bis(5'-nucleosyl)tetraphosphate into two nucleotides.
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    GO:0000302    response to reactive oxygen species    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 a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
cellular component
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AP4A_HUMAN | P505831xsa 1xsb 3u53 4ick 4ijx

(-) Related Entries Specified in the PDB File

1xsa THE SAME PROTEIN(E63A) OF APO STRUCTURE
1xsb THE SAME PROTEIN(E63A) OF ATP STRUCTURE IN COMPLEX WITH ATP