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(-) Description

Title :  S. CEREVISIAE DBP5 BOUND TO RNA AND MANT-ADP BEF3
 
Authors :  M. K. Merchant, Y. Modis
Date :  05 Nov 15  (Deposition) - 24 Feb 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fluorescent, Nucleotide, Mant, Adp, Rna Helicase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. V. Wong, W. Cao, J. Voros, M. Merchant, Y. Modis, D. D. Hackney, B. Montpetit, E. M. De La Cruz
Pi Release Limits The Intrinsic And Rna-Stimulated Atpase Cycles Of Dead-Box Protein 5 (Dbp5).
J. Mol. Biol. V. 428 492 2016
PubMed-ID: 26730886  |  Reference-DOI: 10.1016/J.JMB.2015.12.018

(-) Compounds

Molecule 1 - ATP-DEPENDENT RNA HELICASE DBP5
    Chains: A
    EC Number: 3.6.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 91-481
    Gene: DBP5, RAT8, SCY_5119
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN YJM789)
    Organism Taxid: 307796
    Synonym: DEAD BOX PROTEIN 5,HELICASE CA5/6,RIBONUCLEIC ACID- TRAFFICKING PROTEIN 8
 
Molecule 2 - RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN YJM789)
    Organism Taxid: 307796

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1BEF1Ligand/IonBERYLLIUM TRIFLUORIDE ION
2M2A1Ligand/Ion[(2~{R},3~{R},4~{R},5~{S})-2-(6-AMINOPURIN-9-YL)-4-OXIDANYL-5-[[OXIDANYL(PHOSPHONOOXY)PHOSPHORYL]OXYMETHYL]OXOLAN-3-YL] 2-(METHYLAMINO)BENZOATE
3MG2Ligand/IonMAGNESIUM ION
4NO32Ligand/IonNITRATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:94 , MET A:110 , PHE A:112 , LYS A:114 , GLN A:119 , GLY A:141 , THR A:142 , GLY A:143 , LYS A:144 , THR A:145 , GLU A:184 , ASP A:395 , ARG A:429 , PHE A:430 , MG A:502 , BEF A:503 , HOH A:620 , HOH A:687 , HOH A:697 , HOH A:706 , HOH A:724 , HOH A:757 , HOH A:766 , HOH A:786binding site for residue M2A A 501
2AC2SOFTWAREM2A A:501 , BEF A:503 , HOH A:620 , HOH A:626 , HOH A:692 , HOH A:697binding site for residue MG A 502
3AC3SOFTWARESER A:140 , GLY A:141 , LYS A:144 , GLU A:240 , GLY A:393 , ARG A:426 , ARG A:429 , M2A A:501 , MG A:502 , HOH A:626 , HOH A:692 , HOH A:695 , HOH A:697 , HOH A:789binding site for residue BEF A 503
4AC4SOFTWAREARG A:132 , ASN A:288 , ARG A:463 , PRO A:465 , HOH A:742binding site for residue NO3 A 504
5AC5SOFTWARELYS A:105 , PHE A:188 , LYS A:258 , ARG A:259binding site for residue NO3 A 505
6AC6SOFTWAREASP A:264 , HOH A:605 , HOH A:610 , HOH A:694 , HOH A:805 , HOH A:858binding site for residue MG A 506

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:129 -Pro A:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ELX)

(-) 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    
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(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:391
                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhh.....hhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhh......eeee..............eeeehhhhhhhhhhh.........eeeeehhhhhhhh.hhhhhhhhhhh......eeeeee...hhhhhhhhhhhh...eee..hhhhh....eeeeeee..hhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhh....eeee.hhhh.......eeeeee...........hhhhhhhhhh........eeeeeee.hhhhhhhhhhhhhhh.....ee....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5elx A  91 AKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEMTRVPTDDWDEVEKIVKKVLK 481
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Chain B from PDB  Type:DNA/RNA  Length:6
                                      
                 5elx B   1 UUUUUU   6
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 5ELX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 39)

Asymmetric/Biological Unit(hide GO term definitions)

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  DBP5_YEAS7 | A6ZNQ1
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  DBP5_YEAST | P20449
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 Related Entries

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

UniProtKB/Swiss-Prot
        DBP5_YEAST | P20449: 2kbe 2kbf 3gfp 3peu 3pev 3pew 3pey 3rrm 3rrn

(-) Related Entries Specified in the PDB File

3pey 3PEY CONTAINS THE SAME DEAD-BOX HELICASE BOUND TO RNA AND THE NON- FLUORESCENT ADP BEF3.