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(-) Description

Title :  EOSINOPHIL-DERIVED NEUROTOXIN (EDN) - SULPHATE COMPLEX
 
Authors :  D. D. Leonidas, E. Boix, R. Prill, M. Suzuki, R. Turton, K. Minson, G. J. Swaminathan, R. J. Youle, K. R. Acharya
Date :  02 Jan 01  (Deposition) - 31 May 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Rnase-2, Rnase Us, Ribonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. D. Leonidas, E. Boix, R. Prill, M. Suzuki, R. Turton, K. Minson, G. J. Swaminathan, R. J. Youle, K. R. Acharya
Mapping The Ribonucleolytic Active Site Of Eosinophil-Derived Neurotoxin (Edn): High Resolution Crystal Structures Of Edn Complexes With Adenylic Nucleotide Inhibitors
J. Biol. Chem. V. 276 15009 2001
PubMed-ID: 11154698  |  Reference-DOI: 10.1074/JBC.M010585200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EOSINOPHIL-DERIVED NEUROTOXIN
    CellEOSINOPHIL
    Cellular LocationSECRETORY GRANULES
    ChainsA
    EC Number3.1.27.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    OrganelleGRANULE
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRNASE-2, RNASE-US, EDN
    TissueBLOOD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:14 , HIS A:15 , HIS A:129 , LEU A:130 , HOH A:2015 , HOH A:2110BINDING SITE FOR RESIDUE SO4 A 957
2AC2SOFTWAREARG A:36 , LYS A:38 , ASN A:39 , GLN A:40BINDING SITE FOR RESIDUE SO4 A 958

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:83
2A:37 -A:96
3A:55 -A:111
4A:62 -A:71

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HI2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_059820H100QRNAS2_HUMANPolymorphism8012891AH73Q
2UniProtVAR_013150H156NRNAS2_HUMANPolymorphism146887874AH129N

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_PANCREATICPS00127 Pancreatic ribonuclease family signature.RNAS2_HUMAN64-70  1A:37-43

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003046251ENSE00001285128chr14:21423611-2142369585RNAS2_HUMAN-00--
1.2ENST000003046252ENSE00001124161chr14:21423926-21424595670RNAS2_HUMAN1-1631631A:0-134135

(-) 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:135
 aligned with RNAS2_HUMAN | P10153 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:135
                                    36        46        56        66        76        86        96       106       116       126       136       146       156     
          RNAS2_HUMAN    27 VKPPQFTWAQWFETQHINMTSQQCTNAMQVINNYQRRCKNQNTFLLTTFANVVNVCGNPNMTCPSNKTRKNCHHSGSQVPLIHCNLTTPSPQNISNCRYAQTPANMFYIVACDNRDQRRDPPQYPVVPVHLDRII 161
               SCOP domains d1hi2a_ A: Eosinophil-derived neurotoxin (EDN)                                                                                          SCOP domains
               CATH domains 1hi2A00 A:0-134 P-30 Protein                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh.....hhhhhhhhhhhhhh....eeeee..hhhhhhhhh...............eee....eeeeeeeeee....hhhhheeeeeeeee.eeeeeee...........eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------Q-------------------------------------------------------N----- SAPs(SNPs)
                    PROSITE -------------------------------------RNASE_P------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: A:0-134 UniProt: 1-163 [INCOMPLETE]                                                                                      Transcript 1
                 1hi2 A   0 MKPPQFTWAQWFETQHINMTSQQCTNAMQVINNYQRRCKNQNTFLLTTFANVVNVCGNPNMTCPSNKTRKNCHHSGSQVPLIHCNLTTPSPQNISNCRYAQTPANMFYIVACDNRDQRRDPPQYPVVPVHLDRII 134
                                     9        19        29        39        49        59        69        79        89        99       109       119       129     

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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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HI2)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RNAS2_HUMAN | P10153)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0004522    ribonuclease A activity    Catalysis of the endonucleolytic cleavage of RNA to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0006401    RNA catabolic process    The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:1903955    positive regulation of protein targeting to mitochondrion    Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
cellular component
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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)

UniProtKB/Swiss-Prot
        RNAS2_HUMAN | P101531gqv 1hi3 1hi4 1hi5 1k2a 2bex 2bzz 2c01 2c02 2c05 5e13

(-) Related Entries Specified in the PDB File

1hi3 EOSINOPHIL-DERIVED NEUROTOXIN (EDN) - ADENOSINE-2'-5'-DIPHOSPHATE COMPLEX
1hi4 EOSINOPHIL-DERIVED NEUROTOXIN (EDN) - ADENOSINE-3'-5'-DIPHOSPHATE COMPLEX
1hi5 EOSINOPHIL-DERIVED NEUROTOXIN (EDN) - ADENOSINE-5'-DIPHOSPHATE COMPLEX