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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PURPLE ACID PHOSPHATASE WITH AN INHIBITORY CONFORMATION OF THE REPRESSION LOOP
 
Authors :  N. Straeter, B. Jasper, B. Krebs
Date :  27 Apr 05  (Deposition) - 24 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  X
Keywords :  Metallophosphatase, Dinuclear Metal Site, Trap, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Strater, B. Jasper, M. Scholte, B. Krebs, A. P. Duff, D. B. Langley, R. Han, B. A. Averill, H. C. Freeman, J. M. Guss
Crystal Structures Of Recombinant Human Purple Acid Phosphatase With And Without An Inhibitory Conformation Of The Repression Loop.
J. Mol. Biol. V. 351 233 2005
PubMed-ID: 15993892  |  Reference-DOI: 10.1016/J.JMB.2005.04.014

(-) Compounds

Molecule 1 - TARTRATE-RESISTANT ACID PHOSPHATASE TYPE 5
    ChainsX
    EC Number3.1.3.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPURPLE ACID PHOSPHATASE, TR-AP, TRATPASE, TARTRATE-RESISTANT ACID ATPASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit X

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1FE22Ligand/IonFE (II) ION
2SO41Ligand/IonSULFATE ION
3ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP X:12 , ASP X:50 , TYR X:53 , ASP X:145 , HIS X:221 , FE2 X:1306 , HOH X:2080BINDING SITE FOR RESIDUE FE2 X1305
2AC2SOFTWAREASP X:50 , ASP X:145 , HIS X:184 , HIS X:219 , FE2 X:1305 , HOH X:2080 , HOH X:2110BINDING SITE FOR RESIDUE FE2 X1306
3AC3SOFTWAREHIS X:22 , GLU X:67 , ASP X:71BINDING SITE FOR RESIDUE ZN X1307
4AC4SOFTWAREARG X:79 , SER X:106 , LYS X:107 , ARG X:108 , HOH X:2147BINDING SITE FOR RESIDUE SO4 X1308

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1X:140 -X:198

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala X:19 -Pro X:20
2Tyr X:53 -Phe X:54

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (11, 11)

Asymmetric/Biological Unit (11, 11)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_065920K52MPPA5_HUMANDisease (SPENCDI)  ---XK31M
02UniProtVAR_065921T89IPPA5_HUMANDisease (SPENCDI)387906668XT68I
03UniProtVAR_065922G109RPPA5_HUMANDisease (SPENCDI)781050795XG88R
04UniProtVAR_020602V148MPPA5_HUMANPolymorphism2305799XV127M
05UniProtVAR_020603V200MPPA5_HUMANPolymorphism2229531XV179M
06UniProtVAR_065923L201PPPA5_HUMANDisease (SPENCDI)387906672XL180P
07UniProtVAR_065924G215RPPA5_HUMANDisease (SPENCDI)781199182XG194R
08UniProtVAR_029288V221IPPA5_HUMANPolymorphism2229532XV200I
09UniProtVAR_065925D241NPPA5_HUMANDisease (SPENCDI)  ---XD220N
10UniProtVAR_065926N262HPPA5_HUMANDisease (SPENCDI)  ---XN241H
11UniProtVAR_065927M264KPPA5_HUMANDisease (SPENCDI)387906670XM243K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BQ8)

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002187581ENSE00001484931chr19:11689801-11689659143PPA5_HUMAN-00--
1.2bENST000002187582bENSE00001515028chr19:11689472-1168940073PPA5_HUMAN-00--
1.3bENST000002187583bENSE00001363729chr19:11688494-1168840887PPA5_HUMAN-00--
1.4ENST000002187584ENSE00000683857chr19:11688132-11687872261PPA5_HUMAN1-87871X:1-6666
1.5ENST000002187585ENSE00000683853chr19:11687658-11687531128PPA5_HUMAN88-130431X:67-10943
1.6ENST000002187586ENSE00000683849chr19:11687403-11687058346PPA5_HUMAN130-2451161X:109-224116
1.7ENST000002187587ENSE00001330055chr19:11686067-11685477591PPA5_HUMAN246-325801X:225-30480

(-) 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 X from PDB  Type:PROTEIN  Length:304
 aligned with PPA5_HUMAN | P13686 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:304
                                    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_HUMAN    22 ATPALRFVAVGDWGGVPNAPFHTAREMANAKEIARTVQILGADFILSLGDNFYFTGVQDINDKRFQETFEDVFSDRSLRKVPWYVLAGNHDHLGNVSAQIAYSKISKRWNFPSPFYRLHFKIPQTNVSVAIFMLDTVTLCGNSDDFLSQQPERPRDVKLARTQLSWLKKQLAAAREDYVLVAGHYPVWSIAEHGPTHCLVKQLRPLLATYGVTAYLCGHDHNLQYLQDENGVGYVLSGAGNFMDPSKRHQRKVPNGYLRFHYGTEDSLGGFAYVEISSKEMTVTYIEASGKSLFKTRLPRRARP 325
               SCOP domains d2bq8x_ X: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2bq8X00 X:1-304  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee............hhhhhhhhhhhhhhhhhhh..eeee...............hhhhhhh.....hhhhhh..eee..hhhhhh.hhhhhhhhhhh...ee.....eeeeee......eeeeee.hhhhhhh..............hhhhhhhhhhhhhhhhhhh...eeeee.............hhhhhhhhhhhhhhh...eeee.....eeeee.....eeeee...........hhhhh....eeeee.......eeeeeee...eeeeeeee....eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------M------------------------------------I-------------------R--------------------------------------M---------------------------------------------------MP-------------R-----I-------------------N--------------------H-K------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: X:1-66 UniProt: 1-87 [INCOMPLETE]                  Exon 1.5  PDB: X:67-109 UniProt: 88-130    -------------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: X:225-304 UniProt: 246-325                                        Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: X:109-224 UniProt: 130-245                                                                           -------------------------------------------------------------------------------- Transcript 1 (2)
                 2bq8 X   1 ATPALRFVAVGDWGGVPNAPFHTAREMANAKEIARTVQILGADFILSLGDNFYFTGVQDINDKRFQETFEDVFSDRSLRKVPWYVLAGNHDHLGNVSAQIAYSKISKRWNFPSPFYRLHFKIPQTNVSVAIFMLDTVTLCGNSDDFLSQQPERPRDVKLARTQLSWLKKQLAAAREDYVLVAGHYPVWSIAEHGPTHCLVKQLRPLLATYGVTAYLCGHDHNLQYLQDENGVGYVLSGAGNFMDPSKRHQRKVPNGYLRFHYGTEDSLGGFAYVEISSKEMTVTYIEASGKSLFKTRLPRRARP 304
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300    

   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  (0, 0)

(no "Pfam Domain" information available for 2BQ8)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (PPA5_HUMAN | P13686)
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:0060349    bone morphogenesis    The process in which bones are generated and organized.
    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:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    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:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0032691    negative regulation of interleukin-1 beta production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-1 beta production.
    GO:0032695    negative regulation of interleukin-12 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-12 production.
    GO:0045019    negative regulation of nitric oxide biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.
    GO:0032929    negative regulation of superoxide anion generation    Any process that stops, prevents, or reduces the frequency, rate or extent of enzymatic generation of superoxide by a cell.
    GO:0032720    negative regulation of tumor necrosis factor production    Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production.
    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:0034097    response to cytokine    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 cytokine stimulus.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (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: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.
    GO:0006771    riboflavin metabolic process    The chemical reactions and pathways involving riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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_HUMAN | P136861war

(-) Related Entries Specified in the PDB File

2bq8 CRYSTAL STRUCTURE OF HUMAN PURPLE ACID PHOSPHATASE WITH AN INHIBITORY CONFORMATION OF THE REPRESSION LOOP