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(-) Description

Title :  RIBONUCLEASE 1 DES1-7 CRYSTAL STRUCTURE AT 1.9A
 
Authors :  J. Pous, G. Mallorqui-Fernandez, R. Peracaula, S. S. Terzyan, J. Futami, H. Tada, H. Yamada, M. Seno, R. De Llorens, F. X. Gomis-Ruth, M. Coll
Date :  15 May 00  (Deposition) - 03 May 01  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Human Pancreatic Ribonuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Pous, G. Mallorqui-Fernandez, R. Peracaula, S. S. Terzyan, J. Futami, H. Tada, H. Yamada, M. Seno, R. De Llorens, F. X. Gomis-Ruth, M. Coll
Three-Dimensional Crystal Structure Of Human Rnase 1Dn7 At 1. 9A Resolution
Acta Crystallogr. , Sect. D V. 57 498 2001
PubMed-ID: 11264578  |  Reference-DOI: 10.1107/S0907444901001147

(-) Compounds

Molecule 1 - RIBONUCLEASE 1
    Chains: A
    EC Number: 3.1.27.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organ: PANCREAS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RNASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1E21)

(-) Sites  (0, 0)

(no "Site" information available for 1E21)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:26 -A:84
2A:40 -A:95
3A:58 -A:110
4A:65 -A:72

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:92 -Pro A:93
2Ser A:113 -Pro A:114

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E21)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_PANCREATICPS00127 Pancreatic ribonuclease family signature.RNAS1_HUMAN68-74  1A:40-46

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003979701cENSE00001915577chr14:21271007-2127095652RNAS1_HUMAN-00--
1.2cENST000003979702cENSE00001530999chr14:21270478-2127040871RNAS1_HUMAN-00--
1.3aENST000003979703aENSE00001837426chr14:21270252-21269542711RNAS1_HUMAN1-1651651A:7-126120

(-) 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    
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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:120
 aligned with RNAS1_HUMAN | P07998 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:120
                                    44        54        64        74        84        94       104       114       124       134       144       154
          RNAS1_HUMAN    35 KFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVED 154
               SCOP domains d1e21a_ A: Ribonuclease A (also ribonuclease B, S)                                                                       SCOP domains
               CATH domains 1e21A00 A:7-125 P-30 Protein                                                                                           - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhh..........hhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee......eeeee....................eeee.........eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------RNASE_P-------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3a  PDB: A:7-126 UniProt: 1-165 [INCOMPLETE]                                                                      Transcript 1
                 1e21 A   7 AFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVED 126
                                    16        26        36        46        56        66        76        86        96       106       116       126
   Legend:   → Mismatch (orange background)
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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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E21)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RNAS1_HUMAN | P07998)
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: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).
    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.
biological process
    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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
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.

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  Cis Peptide Bonds
    Ser A:113 - Pro A:114   [ RasMol ]  
    Tyr A:92 - Pro A:93   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        RNAS1_HUMAN | P07998: 1dza 1h8x 1z7x 2e0j 2e0l 2e0m 2e0o 2k11 2q4g 3f8g 4kxh

(-) Related Entries Specified in the PDB File

1h8x DOMAIN-SWAPPED DIMER OF A HUMAN PANCREATIC RIBONUCLEASE VARIANT