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(-) Description

Title :  S1 NUCLEASE FROM ASPERGILLUS ORYZAE IN COMPLEX WITH 2'-DEOXYADENOSINE-5'-THIO-MONOPHOSPHATE (5'DAMP(S)).
 
Authors :  T. Koval, L. H. Oestergaard, J. Dohnalek
Date :  14 Dec 15  (Deposition) - 28 Dec 16  (Release) - 11 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Endonuclease, Zinc Dependent, Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Koval, L. H. Stergaard, J. Lehmbeck, A. Nrgaard, P. Lipovova, J. Duskova, T. Skalova, M. Trundova, P. Kolenko, K. Fejfarova, J. Stransky, L. Svecova, J. Hasek, J. Dohnalek
Structural And Catalytic Properties Of S1 Nuclease From Aspergillus Oryzae Responsible For Substrate Recognition, Cleavage, Non-Specificity, And Inhibition.
Plos One V. 11 68832 2016
PubMed-ID: 28036383  |  Reference-DOI: 10.1371/JOURNAL.PONE.0168832

(-) Compounds

Molecule 1 - NUCLEASE S1
    Chains: A
    EC Number: 3.1.30.1
    Engineered: YES
    Expression System: ASPERGILLUS ORYZAE
    Expression System Taxid: 5062
    Gene: NUCS, AO090001000075
    Organism Common: YELLOW KOJI MOLD
    Organism Scientific: ASPERGILLUS ORYZAE RIB40
    Organism Taxid: 510516
    Other Details: MATURE PROTEIN WITHOUT SIGNAL SEQUENCE.
    Synonym: DEOXYRIBONUCLEASE S1,ENDONUCLEASE S1,SINGLE-STRANDED- NUCLEATE ENDONUCLEASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1AS1Ligand/Ion2-DEOXY-ADENOSINE -5'-THIO-MONOPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZN3Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:21 , HIS A:26 , ASP A:139 , ZN A:402 , HOH A:1112 , HOH A:1148binding site for residue ZN A 401
2AC2SOFTWAREASP A:65 , HIS A:80 , HIS A:135 , ASP A:139 , ZN A:401 , HOH A:1148binding site for residue ZN A 402
3AC3SOFTWAREHIS A:145 , HIS A:168 , ASP A:172 , AS A:601 , HOH A:803 , HOH A:1112binding site for residue ZN A 403
4AC4SOFTWARELYS A:68 , TYR A:69 , PHE A:81 , ASP A:83 , LEU A:144 , HIS A:145 , GLU A:147 , ALA A:151 , GLY A:152 , ASN A:154 , HIS A:168 , ASP A:172 , ZN A:403 , HOH A:803 , HOH A:1068 , HOH A:1112 , HOH A:1188binding site for residue AS A 601
5AC5SOFTWAREPHE A:44 , ASN A:47 , ILE A:48 , PRO A:121 , ASN A:122 , ALA A:245 , ASN A:248 , NAG A:502binding site for residue GOL A 701
6AC6SOFTWAREASN A:112 , ILE A:116 , GLU A:119 , GLU A:255 , ASP A:258 , HOH A:1021 , HOH A:1074 , HOH A:1149 , HOH A:1167binding site for Mono-Saccharide NAG A 501 bound to ASN A 112
7AC7SOFTWAREASN A:122 , GLU A:150 , GLY A:155 , ILE A:156 , ALA A:245 , ASN A:248 , GOL A:701 , HOH A:1032 , HOH A:1056 , HOH A:1102 , HOH A:1168binding site for Mono-Saccharide NAG A 502 bound to ASN A 248

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:92 -A:236
2A:100 -A:105

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:88 -Pro A:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FBC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FBC)

(-) Exons   (0, 0)

(no "Exon" information available for 5FBC)

(-) 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:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhh....hhhhhhhhh.............hhhhhh....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..eeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhh.......hhhhhhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fbc A  21 WGNLGHETVAYIAQSFVASSTESFCQNILGDDSTSYLANVATWADTYKYTDAGEFSKPYHFIDAQDNPPQSCGVDYDRDCGSAGCSISAIQNYTNILLESPNGSEALNALKFVVHIIGDIHQPLHDENLEAGGNGIDVTYDGETTNLHHIWDTNMPEEAAGGYSLSVAKTYADLLTERIKTGTYSSKKDSWTDGIDIKDPVSTSMIWAADANTYVCSTVLDDGLAYINSTDLSGEYYDKSQPVFEELIAKAGYRLAAWLDLIASQPS 287
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 5FBC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FBC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FBC)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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    Pro A:88 - Pro A:89   [ RasMol ]  
 

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  NUS1_ASPOR | P24021
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 Related Entries

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

UniProtKB/Swiss-Prot
        NUS1_ASPOR | P24021: 5fb9 5fba 5fbb 5fbd 5fbf 5fbg

(-) Related Entries Specified in the PDB File

5fb9 5FB9 CONTAINS THE SAME PROTEIN WITH UNOCCUPIED ACTIVE SITE
5fba 5FBA CONTAINS THE SAME PROTEIN IN COMPLEX WITH PHOSPHATE
5fbb 5FBB CONTAINS THE SAME PROTEIN IN COMPLEX WITH PHOSPHATE AND ADENOSINE 5'-MONOPHOSPHATE
5fbd 5FBD CONTAINS THE WILD TYPE OF THE SAME PROTEIN IN COMPLEX WITH PHOSPHATE AND 2'-DEOXYCYTIDINE
5fbf 5FBF CONTAINS THE WILD TYPE OF THE SAME PROTEIN IN COMPLEX WITH TWO MOLECULES OF 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
5fbg 5FBG CONTAINS THE D65N MUTANT OF THE SAME PROTEIN IN COMPLEX WITH PHOSPHATE, 2'-DEOXYCYTIDINE AND 2'-DEOXY-GUANOSINE