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(-) Description

Title :  HUMAN ADENOSINE DEAMINASE ACTING ON DSRNA (ADAR2) BOUND TO DSRNA SEQUENCE DERIVED FROM S. CEREVISIAE BDF2 GENE WITH AC MISMATCH AT REACTION SITE
 
Authors :  M. M. Matthews, A. J. Fisher, P. A. Beal
Date :  20 Jan 16  (Deposition) - 13 Apr 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.09
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
    Chains: A, D
    EC Number: 3.5.4.37
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Common: YEAST
    Expression System Plasmid: PSC
    Expression System Strain: BCY123
    Expression System Taxid: 4932
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 299-701
    Gene: ADARB1, ADAR2, DRADA2, RED1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RNA-EDITING DEAMINASE 1, RNA-EDITING ENZYME 1, DSRNA ADENOSINE DEAMINASE
 
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')
    Chains: B
    Engineered: YES
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synthetic: YES
 
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')
    Chains: C
    Engineered: YES
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synthetic: YES

 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
1AC1SOFTWAREILE A:397 , ARG A:400 , ARG A:401 , THR A:513 , LYS A:519 , ARG A:522 , 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:690binding site for residue IHP A 801
2AC2SOFTWAREHIS A:394 , GLU A:396 , 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: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 , GLU D:396 , CYS D:451 , CYS D:516 , HOH D:901binding site for residue ZN D 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HP3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5HP3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HP3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HP3)

(-) Exons   (0, 0)

(no "Exon" information available for 5HP3)

(-) 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:394
                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhhh....hhhhh...eeeeeee........eeeeeee.....hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....eee....eeeeee..................................eeee.....eee........hhhhhhhh...eeehhhhhhhhhhhhh.hhhhhh.......eeeeee....hhhhhhhhhhhhhh..............eeee..............eeeeee......eeee..............hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hp3 A 307 RQPIPSEGLQLHLPQVLADAVSRLVLGKFGDLTDNFSSPHARRKVLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAEIISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLYISTSPCGDARIFSPHEPILEEPADRHPNRKARGQLRTKIESGEGTIPVRSNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFSSIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQPGKAPNFSVNWTVGDSAIEVINATTGKDELGRASRLCKHALYCRWMRVHGKVPSHLLRSKITKPNVYHESKLAAKEYQAAKARLFTAFIKAGLGAWVEKPTEQDQFSLT 700
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696    


Chain B from PDB  Type:RNA  Length:23
                                                       
                 5hp3 B   1 UUCCCCACAUUxGACGUUCAGUC  23
                                    10 |      20   
                                      12-8AZ       


Chain C from PDB  Type:RNA  Length:23
                                                       
                 5hp3 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.....hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh........eee.....eee....eeeeee.....hhhhh........................eee......eee........hhhhhh......eehhhhhhhhhhhhh.hhhhhh.........eeee....hhhhhhhhhhhhhh..............eeee..............eeeeee......eeee..............hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hp3 D 304 TPSRQPIPSEGLQLHLPQVLADAVSRLVLGKFGDLTDNFSSPHARRKVLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAEIISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLYISTSPCGDARIFSPHEPILEEPADRHPNRKARGQLRTKIESGEGTIPVRSNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFSSIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQPGKAPNFSVNWTVGDSAIEVINATTGKDELGRASRLCKHALYCRWMRVHGKVPSHLLRSKITKPNVYHESKLAAKEYQAAKARLFTAFIKAGLGAWVEKPTEQDQFSLT 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 5HP3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HP3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HP3)

(-) Gene Ontology  (24, 24)

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  5hp3
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 Related Entries

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

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        RED1_HUMAN | P78563: 1zy7 5ed1 5ed2 5hp2

(-) Related Entries Specified in the PDB File

5ed1 5ed2 5hp2