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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PRP43P DEAH-BOX RNA HELICASE IN COMPLEX WITH CDP
 
Authors :  J. Robert-Paganin, S. Rety, N. Leulliot
Date :  04 May 16  (Deposition) - 22 Feb 17  (Release) - 22 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.94
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rna Helicase, Prp43P, Deah/Rha, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Robert-Paganin, M. Halladjian, M. Blaud, S. Lebaron, L. Delbos, F. Chardon, R. Capeyrou, O. Humbert, Y. Henry, A. K. Henras, S. Rety, N. Leulliot
Functional Link Between Deah/Rha Helicase Prp43 Activation And Atp Base Binding.
Nucleic Acids Res. V. 45 1539 2017
PubMed-ID: 28180308  |  Reference-DOI: 10.1093/NAR/GKW1233

(-) Compounds

Molecule 1 - PRE-MRNA-SPLICING FACTOR ATP-DEPENDENT RNA HELICASE PRP43
    Chains: A, B
    EC Number: 3.6.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PRP43, YGL120C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: HELICASE JA1

 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  (5, 7)

Asymmetric Unit (5, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CDP2Ligand/IonCYTIDINE-5'-DIPHOSPHATE
3GOL1Ligand/IonGLYCEROL
4MG2Ligand/IonMAGNESIUM ION
5NI1Ligand/IonNICKEL (II) ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CDP1Ligand/IonCYTIDINE-5'-DIPHOSPHATE
3GOL1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2CDP1Ligand/IonCYTIDINE-5'-DIPHOSPHATE
3GOL-1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:118 , GLY A:119 , SER A:120 , GLY A:121 , LYS A:122 , THR A:123 , THR A:124 , SER A:155 , VAL A:156 , ARG A:159 , PHE A:357 , THR A:384 , ASP A:386 , ARG A:430 , MG A:802 , HOH A:901 , HOH A:903binding site for residue CDP A 801
2AC2SOFTWARETHR A:123 , GLU A:216 , SER A:382 , CDP A:801 , HOH A:901 , HOH A:902 , HOH A:903 , HOH A:904binding site for residue MG A 802
3AC3SOFTWARELEU A:549 , VAL A:551 , GLU A:698 , THR A:709binding site for residue GOL A 803
4AC4SOFTWARETYR A:345 , GLY A:346 , THR A:376binding site for residue ACT A 804
5AC5SOFTWAREHIS A:479 , HIS A:606binding site for residue NI A 805
6AC6SOFTWAREGLU B:117 , THR B:118 , GLY B:119 , SER B:120 , GLY B:121 , LYS B:122 , THR B:123 , THR B:124 , SER B:155 , VAL B:156 , ARG B:159 , PHE B:357 , THR B:384 , ASP B:386 , ARG B:430 , MG B:802 , HOH B:901 , HOH B:902 , HOH B:903 , HOH B:906binding site for residue CDP B 801
7AC7SOFTWARETHR B:123 , GLU B:216 , SER B:382 , CDP B:801 , HOH B:902 , HOH B:903 , HOH B:905 , HOH B:906binding site for residue MG B 802

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JPT)

(-) 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:745
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhh........................hhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhh.......eeeee..eee......eeeeehhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhh....eee.......eeee.......hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhh...........eeeeee.hhhh.......eeeeee..eeeeeeee....eeeeeeee.hhhhhhhhhhhhhh...eeeee..hhhhhhh.......hhhhh..hhhhhhhhhhh..............hhhhhhhhhhhhhhh.........hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhh..eeee....eee.hhh.eeee...........eeeeeeeee...eeeeeeee.hhhhhhhhh....hhhhh..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jpt A   3 SKRRFSSEHPDPVETSIPEQAAEIAEELSKQHPLPSEEPLVHHDAGEFKGLQRHHTSAEEAQKLEDGKINPFTGREFTPKYVDILKIRRELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFENKTSNKTILKYMTDGMLLREAMEDHDLSRYSCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSATLDAEKFQRYFNDAPLLAVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSSTVLELKKLGIDDLVHFDFMDPPAPETMMRALEELNYLACLDDEGNLTPLGRLASQFPLDPMLAVMLIGSFEFQCSQEILTIVAMLSVPNVFIRPTKDKKRADDAKNIFAHPDGDHITLLNVYHAFKSDEAYEYGIHKWCRDHYLNYRSLSAADNIRSQLERLMNRYNLELNTTDYESPKYFDNIRKALASGFFMQVAKKRSGGYITVKDNQDVLIHPSTVLGHDAEWVIYNEFVLTSKNYIRTVTSVRPEWLIEIAPAYYDLSNFQKGDVKLSLERIKEKVDR 749
                                    12        22        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       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662   ||  674       684       694       704       714       724       734       744     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 666|                                                                                
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  669                                                                                


Chain B from PDB  Type:PROTEIN  Length:741
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhh..........................hhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhh.......eeeee..eee......eeeeehhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhh....eee.......eeee.......hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhh...........eeeeee.hhhh.......eeeeee..eeeeeeee....eeeeeeee.hhhhhhhhhhhhhh...eeeee..hhhhhhhh......hhhhhh.hhhhhhhhhhh..............hhhhhhhhhhhhhhh.........hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhh..eee...eee.....eeee...........eeeeeeeee...eeeeeeee.hhhhhhhhh....hhhhh..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jpt B   3 SKRRFSSEHPDPVETSIPEQAAEIAEELSKQHPLPSEEPLVHHDAGEFKGLQRHHTSAEEAQKLEDGKINPFTGREFTPKYVDILKIRRELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFENKTSNKTILKYMTDGMLLREAMEDHDLSRYSCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSATLDAEKFQRYFNDAPLLAVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSSTVLELKKLGIDDLVHFDFMDPPAPETMMRALEELNYLACLDDEGNLTPLGRLASQFPLDPMLAVMLIGSFEFQCSQEILTIVAMLSVPNVFIRPTKDKKRADDAKNIFAHPDGDHITLLNVYHAFKSDEAYEYGIHKWCRDHYLNYRSLSAADNIRSQLERLMNRYNLELNTTDYESPKYFDNIRKALASGFFMQVAKKRGYITVKDNQDVLIHPSTVLGHDAEWVIYNEFVLTSKNYIRTVTSVRPEWLIEIAPAYYDLSNFQKGDVKLSLERIKEKV 747
                                    12        22        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       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662 ||    676       686       696       706       716       726       736       746 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               664|                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                669
   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 5JPT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

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  5jpt
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  PRP43_YEAST | P53131
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 Related Entries

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UniProtKB/Swiss-Prot
        PRP43_YEAST | P53131: 2xau 3kx2 5i8q

(-) Related Entries Specified in the PDB File

2kx2 2xau 5d0u