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(-) Description

Title :  STRUCTURE OF RAT PURPLE ACID PHOSPHATASE
 
Authors :  J. Uppenberg, F. Lindqvist, C. Svensson, B. Ek-Rylander, G. Andersson
Date :  08 Apr 99  (Deposition) - 10 Apr 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Metal Phosphatase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Uppenberg, F. Lindqvist, C. Svensson, B. Ek-Rylander, G. Andersso
Crystal Structure Of A Mammalian Purple Acid Phosphatase.
J. Mol. Biol. V. 290 201 1999
PubMed-ID: 10388567  |  Reference-DOI: 10.1006/JMBI.1999.2896

(-) Compounds

Molecule 1 - PROTEIN (PURPLE ACID PHOSPHATASE)
    ChainsA
    EC Number3.1.3.2
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System VectorBACULOVIRUS
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymTARTRATE RESISTANT ACID PHOSPHATASE, TRAP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:62 , ASN A:97BINDING SITE FOR RESIDUE NAG A 400
2AC2SOFTWAREASP A:52 , ASN A:91 , HIS A:186 , HIS A:221 , FE A:402 , PO4 A:410BINDING SITE FOR RESIDUE FE A 401
3AC3SOFTWAREASP A:14 , ASP A:52 , TYR A:55 , HIS A:221 , HIS A:223 , FE A:401 , PO4 A:410BINDING SITE FOR RESIDUE FE A 402
4AC4SOFTWAREASP A:52 , TYR A:55 , ASN A:91 , HIS A:92 , HIS A:195 , HIS A:221 , HIS A:223 , FE A:401 , FE A:402BINDING SITE FOR RESIDUE PO4 A 410

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:142 -A:200

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:18 -Pro A:19
2Ala A:21 -Pro A:22

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QFC)

(-) 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:287
 aligned with PPA5_RAT | P29288 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:302
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321  
             PPA5_RAT    22 TAPASTLRFVAVGDWGGVPNAPFHTAREMANAKEIARTVQIMGADFIMSLGDNFYFTGVHDANDKRFQETFEDVFSDRALRNIPWYVLAGNHDHLGNVSAQIAYSKISKRWNFPSPYYRLRFKVPRSNITVAIFMLDTVMLCGNSDDFVSQQPEMPRDLGVARTQLSWLKKQLAAAKEDYVLVAGHYPIWSIAEHGPTRCLVKNLRPLLAAYGVTAYLCGHDHNLQYLQDENGVGYVLSGAGNFMDPSVRHQRKVPNGYLRFHYGSEDSLGGFTYVEIGSKEMSITYVEASGKSLFKTSLPR 323
               SCOP domains d1qfca_ A: Mammalian purple acid phosphatase                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1qfcA00 A:1-302  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------Metallophos-1qfcA01 A:7-225                                                                                                                                                                                                ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.............hhhhhhhhhhhhhhhh....eeee................hhhhhhhhh.........eee.....hhh...hhhhhhhhh...........eeeeee......eeeeee..hhhh....---------------....hhhhhhhhhhh....eeeee..............hhhhhh.hhhhhhh...eeee.....eeeee.....eeeee....................eeeee.......eeeeeee...eeeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qfc A   1 TAPASTLRFVAVGDWGGVPNAPFHTAREMANAKEIARTVQIMGADFIMSLGDNFYFTGVHDANDKRFQETFEDVFSDRALRNIPWYVLAGNHDHLGNVSAQIAYSKISKRWNFPSPYYRLRFKVPRSNITVAIFMLDTVMLCGNS---------------VARTQLSWLKKQLAAAKEDYVLVAGHYPIWSIAEHGPTRCLVKNLRPLLAAYGVTAYLCGHDHNLQYLQDENGVGYVLSGAGNFMDPSVRHQRKVPNGYLRFHYGSEDSLGGFTYVEIGSKEMSITYVEASGKSLFKTSLPR 302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    |    -         -|      170       180       190       200       210       220       230       240       250       260       270       280       290       300  
                                                                                                                                                                          145             161                                                                                                                                             

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PPA5_RAT | P29288)
molecular function
    GO:0003993    acid phosphatase activity    Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an acid pH optimum.
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0045453    bone resorption    The process in which specialized cells known as osteoclasts degrade the organic and inorganic portions of bone, and endocytose and transport the degradation products.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0033555    multicellular organismal response to stress    Any process that results in a change in state or activity of a multicellular organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    GO:0007162    negative regulation of cell adhesion    Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
    GO:0001503    ossification    The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
    GO:0030316    osteoclast differentiation    The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0033591    response to L-ascorbic acid    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 L-ascorbic acid (vitamin C) stimulus.
    GO:0070723    response to cholesterol    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 cholesterol stimulus.
    GO:0014070    response to organic cyclic compound    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 organic cyclic compound stimulus.
    GO:0010043    response to zinc ion    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 zinc ion stimulus.
cellular component
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.

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 Related Entries

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

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        PPA5_RAT | P292881qhw

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