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(-) Description

Title :  CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF DNASE I AT 2 ANGSTROMS RESOLUTION
 
Authors :  C. Oefner, D. Suck
Date :  20 Aug 92  (Deposition) - 31 Jan 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Endonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Oefner, D. Suck
Crystallographic Refinement And Structure Of Dnase I At 2 A Resolution.
J. Mol. Biol. V. 192 605 1986
PubMed-ID: 3560229  |  Reference-DOI: 10.1016/0022-2836(86)90280-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DEOXYRIBONUCLEASE I
    ChainsA
    EC Number3.1.21.1
    EngineeredYES
    Organism CommonCOW
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    TissuePANCREAS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric Unit (5, 9)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2CA2Ligand/IonCALCIUM ION
3GLA1Ligand/IonALPHA D-GALACTOSE
4MAN1Ligand/IonALPHA-D-MANNOSE
5NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 14)
No.NameCountTypeFull Name
1BMA6Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3GLA2Ligand/IonALPHA D-GALACTOSE
4MAN2Ligand/IonALPHA-D-MANNOSE
5NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:18 , NAG A:262 , HOH A:417 , HOH A:476BINDING SITE FOR RESIDUE NAG A 261
2AC2SOFTWAREGLU A:244 , NAG A:261 , BMA A:263BINDING SITE FOR RESIDUE NAG A 262
3AC3SOFTWARENAG A:262 , MAN A:264 , BMA A:265 , BMA A:266 , HOH A:581BINDING SITE FOR RESIDUE BMA A 263
4AC4SOFTWAREBMA A:263 , BMA A:265BINDING SITE FOR RESIDUE MAN A 264
5AC5SOFTWAREBMA A:263 , MAN A:264 , BMA A:266 , HOH A:612 , HOH A:618BINDING SITE FOR RESIDUE BMA A 265
6AC6SOFTWAREBMA A:263 , BMA A:265 , GLA A:267BINDING SITE FOR RESIDUE BMA A 266
7AC7SOFTWAREBMA A:266BINDING SITE FOR RESIDUE GLA A 267
8AC8SOFTWAREASP A:201 , THR A:203 , THR A:205 , THR A:207 , HOH A:355 , HOH A:356BINDING SITE FOR RESIDUE CA A 281
9AC9SOFTWAREASP A:99 , ASP A:107 , PHE A:109 , SER A:110 , GLU A:112 , HOH A:408 , HOH A:409BINDING SITE FOR RESIDUE CA A 282

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:101 -A:104
2A:173 -A:209

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DNI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_DNAS1_BOVIN_001 *H143PDNAS1_BOVIN  ---  ---AH121P
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_DNAS1_BOVIN_001 *H143PDNAS1_BOVIN  ---  ---AH121P
   * ID not provided by source

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNASE_I_1PS00919 Deoxyribonuclease I signature 1.DNAS1_BOVIN152-172  1A:130-150
2DNASE_I_2PS00918 Deoxyribonuclease I signature 2.DNAS1_BOVIN189-196  1A:167-174
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNASE_I_1PS00919 Deoxyribonuclease I signature 1.DNAS1_BOVIN152-172  2A:130-150
2DNASE_I_2PS00918 Deoxyribonuclease I signature 2.DNAS1_BOVIN189-196  2A:167-174

(-) Exons   (8, 8)

Asymmetric Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000267841ENSBTAE00000293181chr25:3564711-3564829119DNAS1_BOVIN-00--
1.2ENSBTAT000000267842ENSBTAE00000218065chr25:3565156-3565303148DNAS1_BOVIN1-49491A:1-2727
1.3ENSBTAT000000267843ENSBTAE00000420413chr25:3565639-356572789DNAS1_BOVIN50-79301A:28-5730
1.4ENSBTAT000000267844ENSBTAE00000410212chr25:3565904-356598784DNAS1_BOVIN79-107291A:57-8529
1.5ENSBTAT000000267845ENSBTAE00000218074chr25:3566232-3566347116DNAS1_BOVIN107-146401A:85-124 (gaps)40
1.6ENSBTAT000000267846ENSBTAE00000407443chr25:3566499-3566611113DNAS1_BOVIN146-183381A:124-16138
1.7ENSBTAT000000267847ENSBTAE00000398022chr25:3566701-3566855155DNAS1_BOVIN184-235521A:162-21352
1.8ENSBTAT000000267848ENSBTAE00000425804chr25:3567129-356722597DNAS1_BOVIN235-267331A:213-24533
1.9ENSBTAT000000267849ENSBTAE00000293180chr25:3567369-3567733365DNAS1_BOVIN268-282151A:246-26015

(-) Sequences/Alignments

Asymmetric 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:258
 aligned with DNAS1_BOVIN | P00639 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:260
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282
          DNAS1_BOVIN    23 LKIAAFNIRTFGETKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAVGKLLDYLNQDDPNTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDGCESCGNDSFSREPAVVKFSSHSTKVKEFAIVALHSAPSDAVAEINSLYDVYLDVQQKWHLNDVMLMGDFNADCSYVTSSQWSSIRLRTSSTFQWLIPDSADTTATSTNCAYDRIVVAGSLLQSSVVPGSAAPFDFQAAYGLSNEMALAISDHYPVEVTLT 282
               SCOP domains d3dnia_ A: Deoxyribonuclease I                                                                                                                                                                                                                                       SCOP domains
               CATH domains 3dniA00 A:1-260  [code=3.60.10.10, no name defined]                                                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.hhhh..hhhhhhhhhhhh...eeeeeee.....hhhhhhhhhh........eeee...........eeeeee....eeeeeeee.....--..........eeeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhhh....eeeeee................hhhh....ee.................eeeeee.hhhhhh......ee..hhhhh...hhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------P------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------DNASE_I_1            ----------------DNASE_I_-------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:1-27      Exon 1.3  PDB: A:28-57        ---------------------------Exon 1.5  PDB: A:85-124 (gaps)          -------------------------------------Exon 1.7  PDB: A:162-213 UniProt: 184-235           --------------------------------Exon 1.9        Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.4  PDB: A:57-85       --------------------------------------Exon 1.6  PDB: A:124-161              ---------------------------------------------------Exon 1.8  PDB: A:213-245         --------------- Transcript 1 (2)
                 3dni A   1 LKIAAFNIRTFGETKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAVGKLLDYLNQDDPNTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDGC--CGNDSFSREPAVVKFSSHSTKVKEFAIVALHSAPSDAVAEINSLYDVYLDVQQKWHLNDVMLMGDFNADCSYVTSSQWSSIRLRTSSTFQWLIPDSADTTATSTNCAYDRIVVAGSLLQSSVVPGSAAPFDFQAAYGLSNEMALAISDHYPVEVTLT 260
                                    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
                                                                                                                              101  |                                                                                                                                                            
                                                                                                                                 104                                                                                                                                                            

   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 Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DNI)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (DNAS1_BOVIN | P00639)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0004530    deoxyribonuclease I activity    Catalysis of the endonucleolytic cleavage of DNA to 5'-phosphodinucleotide and 5'-phosphooligonucleotide end products.
    GO:0004536    deoxyribonuclease activity    Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid.
    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.
biological process
    GO:0006308    DNA catabolic process    The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    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: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: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:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DNAS1_BOVIN | P006391atn 1dnk 2a3z 2a40 2a41 2a42 2d1k 2dnj 3cjc 3w3d

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