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(-) Description

Title :  HUMAN ADENOSINE DEAMINASE ACTING ON DSRNA (ADAR2) MUTANT E488Q BOUND TO DSRNA SEQUENCE DERIVED FROM S. CEREVISIAE BDF2 GENE
 
Authors :  M. M. Matthews, A. J. Fisher, P. A. Beal
Date :  20 Oct 15  (Deposition) - 13 Apr 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.77
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D  (1x)
Keywords :  Deaminase, Human, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. M. Matthews, J. M. Thomas, Y. Zheng, K. Tran, K. J. Phelps, A. I. Scott J. Havel, A. J. Fisher, P. A. Beal
Structures Of Human Adar2 Bound To Dsrna Reveal Base-Flipping Mechanism And Basis For Site Selectivity.
Nat. Struct. Mol. Biol. V. 23 426 2016
PubMed-ID: 27065196  |  Reference-DOI: 10.1038/NSMB.3203

(-) Compounds

Molecule 1 - DOUBLE-STRANDED RNA-SPECIFIC EDITASE 1
    ChainsA, D
    EC Number3.5.4.37
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System CommonYEAST
    Expression System PlasmidPSC
    Expression System StrainBCY123
    Expression System Taxid4932
    Expression System Vector TypePLASMID
    FragmentA TO I EDITASE (UNP RESIDUES 327-729)
    GeneADAR2, DRADA2, RED1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymADENOSINE DEAMINASE ACTING ON RNA
 
Molecule 2 - RNA (5'-R(*UP*UP*CP*CP*CP*CP*AP*CP*AP*UP*UP*(8AZ) P*GP*AP*CP*GP*UP*UP*CP*AP*GP*UP*C)-3')
    ChainsB
    EngineeredYES
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SyntheticYES
 
Molecule 3 - RNA (5'- R(*GP*AP*CP*UP*GP*AP*AP*CP*GP*AP*CP*CP*AP*AP*UP*GP*UP*GP*GP*GP*GP*AP* A)-3')
    ChainsC
    EngineeredYES
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)ABC 
Biological Unit 2 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
18AZ1Mod. Nucleotide8-AZA-NEBULARINE-5'-MONOPHOSPHATE
2IHP2Ligand/IonINOSITOL HEXAKISPHOSPHATE
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
18AZ1Mod. Nucleotide8-AZA-NEBULARINE-5'-MONOPHOSPHATE
2IHP1Ligand/IonINOSITOL HEXAKISPHOSPHATE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
18AZ-1Mod. Nucleotide8-AZA-NEBULARINE-5'-MONOPHOSPHATE
2IHP1Ligand/IonINOSITOL HEXAKISPHOSPHATE
3ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:391 , ILE A:397 , ARG A:400 , ARG A:401 , THR A:513 , LYS A:519 , ARG A:522 , GLY A:530 , SER A:531 , LYS A:629 , TYR A:658 , LYS A:662 , TYR A:668 , LYS A:672 , TRP A:687 , GLU A:689 , LYS A:690 , HOH A:901 , HOH A:917binding site for residue IHP A 801
2AC2SOFTWAREHIS A:394 , CYS A:451 , LYS A:483 , CYS A:516 , 8AZ B:12binding site for residue ZN A 802
3AC3SOFTWAREASN D:391 , ILE D:397 , ARG D:400 , ARG D:401 , THR D:513 , LYS D:519 , ARG D:522 , GLY D:530 , SER D:531 , LYS D:629 , TYR D:658 , LYS D:662 , TYR D:668 , LYS D:672 , TRP D:687 , GLU D:689 , LYS D:690binding site for residue IHP D 801
4AC4SOFTWAREHIS D:394 , CYS D:451 , LYS D:483 , CYS D:516 , HOH D:905binding site for residue ZN D 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ED1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5ED1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5ED1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ED1)

(-) Exons   (0, 0)

(no "Exon" information available for 5ED1)

(-) 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:396
                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhhhhh............eeeeeee........eeeeeee.....hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....eee....eeeeee..................................eeee.....eee........hhhhhhhh...eeehhhhhhhhhhhhh.hhhhhhh......eeeeee....hhhhhhhhhhhhhh..............eeee..............eeeeee......eeee..............hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ed1 A 305 PSRQPIPSEGLQLHLPQVLADAVSRLVLGKFGDLTDNFSSPHARRKVLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAEIISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLYISTSPCGDARIFSPHEPILEEPADRHPNRKARGQLRTKIESGQGTIPVRSNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFSSIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQPGKAPNFSVNWTVGDSAIEVINATTGKDELGRASRLCKHALYCRWMRVHGKVPSHLLRSKITKPNVYHESKLAAKEYQAAKARLFTAFIKAGLGAWVEKPTEQDQFSLT 700
                                   314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694      

Chain B from PDB  Type:RNA  Length:23
                                                       
                 5ed1 B   1 UUCCCCACAUUxGACGUUCAGUC  23
                                    10 |      20   
                                      12-8AZ       

Chain C from PDB  Type:RNA  Length:23
                                                       
                 5ed1 C   1 GACUGAACGACCAAUGUGGGGAA  23
                                    10        20   

Chain D from PDB  Type:PROTEIN  Length:397
                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..........hhhhhhhhhhhhhhhhhhhhh....hhhhh...eeeeeee........eeeeeee.eee.hhhhh........eeehhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.....eee....eeeeee.....hhhhh........................eeee.....eee........hhhhhh.....eeehhhhhhhhhhhhh.hhhhhh.......eeeeee....hhhhhhhhhhhhhh..............eeee..............eeeeee......eeee..............hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ed1 D 304 TPSRQPIPSEGLQLHLPQVLADAVSRLVLGKFGDLTDNFSSPHARRKVLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAEIISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLYISTSPCGDARIFSPHEPILEEPADRHPNRKARGQLRTKIESGQGTIPVRSNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFSSIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQPGKAPNFSVNWTVGDSAIEVINATTGKDELGRASRLCKHALYCRWMRVHGKVPSHLLRSKITKPNVYHESKLAAKEYQAAKARLFTAFIKAGLGAWVEKPTEQDQFSLT 700
                                   313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       

   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  (0, 0)

(no "SCOP Domain" information available for 5ED1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ED1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ED1)

(-) Gene Ontology  (24, 24)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RED1_HUMAN | P785631zy7 5ed2 5hp2 5hp3

(-) Related Entries Specified in the PDB File

5ed2