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(-) Description

Title :  IMPROVED REFINEMENT OF THE MTR4 APO CRYSTAL STRUCTURE
 
Authors :  S. J. Johnson, L. L. Taylor
Date :  10 Jul 14  (Deposition) - 03 Dec 14  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.39
Chains :  Asym./Biol. Unit :  A
Keywords :  Rec-A Fold, Winged-Helix-Turn-Helix, Antiparallel-Coiled-Coil, Dshct Domain, Helicase, Nucleotide Binding, Phosphoprotein, Rrna Processing, Tramp, Atp Binding, Nucleus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. L. Taylor, R. N. Jackson, M. Rexhepaj, A. K. King, L. K. Lott, A. Van Hoof, S. J. Johnson
The Mtr4 Ratchet Helix And Arch Domain Both Function To Promote Rna Unwinding.
Nucleic Acids Res. V. 42 13861 2014
PubMed-ID: 25414331  |  Reference-DOI: 10.1093/NAR/GKU1208
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ATP-DEPENDENT RNA HELICASE DOB1
    Chains: A
    EC Number: 3.6.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET151 DIRECTIONAL TOPO
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DOB1, J1158, MTR4, MTR4/YJL050W, YJL050W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: MRNA TRANSPORT REGULATOR MTR4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:263 , TYR A:266 , GLY A:508BINDING SITE FOR RESIDUE PO4 A 1101
2AC2SOFTWARELYS A:416 , HIS A:476 , SER A:477 , THR A:502 , THR A:504BINDING SITE FOR RESIDUE PO4 A 1102
3AC3SOFTWARELYS A:827BINDING SITE FOR RESIDUE PO4 A 1103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QU4)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Lys A:345 -Ser A:346
2Ile A:507 -Gly A:508
3Gly A:526 -Gln A:527

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QU4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QU4)

(-) Exons   (0, 0)

(no "Exon" information available for 4QU4)

(-) 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    
   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:942
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee..................eeeeeeeeeeeee.........................hhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.eeee....ee.....eeeeehhhhhhhhhh..hhhh.eeeeeee.hhhhhh..hhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhh...eeeeee......eeeeee.......eeee......hhhhhhhhhhh..hhhhhhhhhhhhhh....ee....hhhhhhhhhhh..........hhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhh..eeee......hhhhhhhhhhhh....eeee.............eeee...ee......ee.hhhhhhhhhh..........eeeeee.....hhhhhhhhhh............hhhhhhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh....eeeeeeehhheeeeeeeeeeeee................eeeeeeeeeee...hhhhh...................eeeeeeeee...eeeeeeee..........hhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.......................hhhhhhhhhh...........hhhhhh.....hhhhhhhhhhhhhhhhhh..................hhhhhhh...hhhhh........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4qu4 A   79 PVLADSFEQEASREVASKGLTNSETLQVEQDGKVRLSHQVRHQVALPPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASIAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFHLGYNMILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEKKLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVNGKDNYGWGAVVDFAKRINKRNPSAVYTDHESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPITLDSIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKKIDVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRKISEAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCLAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGTFTQICKMTDVYEGSLIRMFKRLEELVKELDVATINSSLKEKMEAVLKLIHRDIVSAGSLY 1072
                                    88    ||  99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359||     398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868   ||  880       890       900       910       920       930       940 ||    966       976       986       996      1006||    1017      1027      1037|| |||1050      1060      1070  
                                         93|                                                                                                                                                                                                                                                                      360|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               872|                                                                942|                                            1007|                         1038| ||||                         
                                          95                                                                                                                                                                                                                                                                       390                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                875                                                                 959                                             1009                          1040 ||||                         
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             1047
   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 4QU4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QU4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QU4)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:526 - Gln A:527   [ RasMol ]  
    Ile A:507 - Gly A:508   [ RasMol ]  
    Lys A:345 - Ser A:346   [ RasMol ]  
 

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  MTR4_YEAST | P47047
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 Related Entries

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

UniProtKB/Swiss-Prot
        MTR4_YEAST | P47047: 2xgj 4u4c 4wfd

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4QU4)