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(-) Description

Title :  STEROID RECEPTOR RNA ACTIVATOR (SRA) MODIFICATION BY THE HUMAN PSEUDOURIDINE SYNTHASE 1 (HPUS1P): RNA BINDING, ACTIVITY, AND ATOMIC MODEL
 
Authors :  T. Huet, S. Thore
Date :  11 Dec 13  (Deposition) - 21 May 14  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nuclear Receptor Coactivator, Steroid Receptor Rna Activator, Pseudouridylation, Nucleus, Mitochondrial, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Huet, F. -A. Miannay, J. R. Patton, S. Thore
Steroid Receptor Rna Activator (Sra) Modification By The Human Pseudouridine Synthase 1 (Hpus1P): Rna Binding, Activity, And Atomic Model
Plos One V. 9 94610 2014
PubMed-ID: 24722331  |  Reference-DOI: 10.1371/JOURNAL.PONE.0094610

(-) Compounds

Molecule 1 - TRNA PSEUDOURIDINE SYNTHASE A, MITOCHONDRIAL
    ChainsA, B
    EC Number5.4.99.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21 DE3 STAR
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN, UNP RESIDUES 83-394
    GenePUS1, PP8985
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTRNA PSEUDOURIDINE(38-40) SYNTHASE, TRNA PSEUDOURIDYLATE SYNTHASE I, TRNA-URIDINE ISOMERASE I

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1DGL1Ligand/IonD-GLUTAMIC ACID
2DLY1Ligand/IonD-LYSINE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1DGL-1Ligand/IonD-GLUTAMIC ACID
2DLY1Ligand/IonD-LYSINE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1DGL1Ligand/IonD-GLUTAMIC ACID
2DLY-1Ligand/IonD-LYSINE
3EDO-1Ligand/Ion1,2-ETHANEDIOL
4PGE-1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:95 , GLY A:379 , THR A:380 , ASP A:383 , ARG B:122BINDING SITE FOR RESIDUE EDO A 401
2AC2SOFTWARELEU A:174 , SER A:176 , ARG A:179 , HOH A:517 , LEU B:174 , SER B:176 , ARG B:179BINDING SITE FOR RESIDUE PGE A 402
3AC3SOFTWAREARG A:144 , THR A:145 , ASP A:146 , VAL A:149 , TYR A:201 , ARG A:295 , LEU A:333 , HOH A:719BINDING SITE FOR RESIDUE DLY A 403
4AC4SOFTWARETHR B:145 , ASP B:146 , VAL B:149 , TYR B:201 , MET B:290 , HIS B:292 , GLN B:293 , ILE B:294 , ARG B:295 , HOH B:751BINDING SITE FOR RESIDUE DGL B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NZ6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp B:350 -Gly B:351

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NZ6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NZ6)

(-) Exons   (0, 0)

(no "Exon" information available for 4NZ6)

(-) 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:305
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.............hhhhhhhhhhhhh...hhhhhhh......ee........eeeeeeeeeee....hhhhhhhh.....eeeeeeee.....hhhhhh..eeeeeeee.hhhh.............hhhhhhhhhhhhhh..eeee.hhhh......hhh.eeeeeeeee...eee..eeeeeeeeee.....hhhhhhhhhhhhhhh....hhhhhhh...............eeeeee.hhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nz6 A  83 KRKIVLLMAYSGKGYHGMQRQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCARTDKGVSAAGQVVSLKVWLIDDILEKINSHLPSHIRILGLKRVTGGFNSKNRCDARTYCYLLPTFAFAHKDRDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPQDPSACRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLERSWGTEKVDVPKAPGLGLVLERVHFEKYNQRFGNLHEPLDWAQEEGKVAAFKEEHIYPTIIGTERDERSMAQWLSTL 394
                                    92       102|      117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347 ||    359       369       379       389     
                                             102|                                                                                                                                                                                                                                              349|                                          
                                              108                                                                                                                                                                                                                                               352                                          

Chain B from PDB  Type:PROTEIN  Length:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee..............hhhhhhhhhhhhh...hhhhhhhhhhhh.ee........eeeeeeeeeee....hhhhhhhh.....eeeeeeeee....hhhhhh.eeeeeeeee.hhh..............hhhhhhhhhhhhhh..eeee.hhhh......hhh.eeeeeeeee...eee..eeeeeeeeee.....hhhhhhhhhhhhhhh....hhhhhhh...............eeeeeeehhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nz6 B  82 SKRKIVLLMAYSGKGYHGMQRNQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCARTDKGVSAAGQVVSLKVWLIDDILEKINSHLPSHIRILGLKRVTGGFNSKNRCDARTYCYLLPTFAFAHKDRDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPQDPSACRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLERSWGTEKVDVPKAPGLGLVLERVHFEKYNQRFGNDGLHEPLDWAQEEGKVAAFKEEHIYPTIIGTERDERSMAQWLSTL 394
                                    91       101 ||    115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385         
                                               103|                                                                                                                                                                                                                                                                                              
                                                108                                                                                                                                                                                                                                                                                              

   Legend:   → Mismatch (orange background)
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    → 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 4NZ6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NZ6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NZ6)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        TRUA_HUMAN | Q9Y6064iqm 4its 4j37 4nz7

(-) Related Entries Specified in the PDB File

4nz7