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(-) Description

Title :  RNASE-L INHIBITOR
 
Authors :  A. Karcher, K. Buttner, B. Martens, R. P. Jansen, K. P. Hopfner
Date :  02 Feb 05  (Deposition) - 19 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Atp-Binding Cassette, Ribosome Biogenesis, Hydrolyase/Translation Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Karcher, K. Buttner, B. Martens, R. P. Jansen, K. P. Hopfner
X-Ray Structure Of Rli, An Essential Twin Cassette Abc Atpase Involved In Ribosome Biogenesis And Hiv Capsid Assembly.
Structure V. 13 649 2005
PubMed-ID: 15837203  |  Reference-DOI: 10.1016/J.STR.2005.02.008
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNASE L INHIBITOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21 CODON PLUS (RIL)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: TWIN CASSETTE ATPASE DOMAIN
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:378 , GLN A:406 , ADP A:593 , HOH A:595 , HOH A:596 , HOH A:597BINDING SITE FOR RESIDUE MG A 591
2AC2SOFTWARESER A:113 , GLN A:165 , GLU A:236 , ADP A:594 , HOH A:598 , HOH A:599 , HOH A:600BINDING SITE FOR RESIDUE MG A 592
3AC3SOFTWARETYR A:349 , PHE A:352 , ASN A:373 , GLY A:374 , ILE A:375 , GLY A:376 , LYS A:377 , THR A:378 , THR A:379 , TYR A:417 , ASP A:448 , GLY A:532 , MG A:591 , HOH A:595 , HOH A:597 , HOH A:650 , HOH A:652 , HOH A:664 , HOH A:673 , HOH A:681 , HOH A:692 , HOH A:705 , HOH A:716 , HOH A:762BINDING SITE FOR RESIDUE ADP A 593
4AC4SOFTWARETYR A:83 , PHE A:88 , ASN A:108 , GLY A:109 , THR A:110 , GLY A:111 , LYS A:112 , SER A:113 , THR A:114 , GLY A:288 , MG A:592 , HOH A:598 , HOH A:599 , HOH A:600 , HOH A:660 , HOH A:697 , HOH A:744BINDING SITE FOR RESIDUE ADP A 594

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:79 -A:128

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YQT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YQT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YQT)

(-) Exons   (0, 0)

(no "Exon" information available for 1YQT)

(-) 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:515
 aligned with Q8U306_PYRFU | Q8U306 from UniProtKB/TrEMBL  Length:590

    Alignment length:515
                                    85        95       105       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       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585     
         Q8U306_PYRFU    76 EEDCVHRYGVNAFVLYRLPVVKEGMVVGIVGPNGTGKSTAVKILAGQLIPNLCGDNDSWDGVIRAFRGNELQNYFEKLKNGEIRPVVKPQYVDLIPKAVKGKVIELLKKADETGKLEEVVKALELENVLDREIQHLSGGELQRVAIAAALLRNATFYFFDEPSSYLDIRQRLNAARAIRRLSEEGKSVLVVEHDLAVLDYLSDIIHVVYGEPGVYGIFSQPKGTRNGINEFLRGYLKDENVRFRPYEIKFTKTGERVEIERETLVTYPRLVKDYGSFRLEVEPGEIKKGEVIGIVGPNGIGKTTFVKMLAGVEEPTEGKIEWDLTVAYKPQYIKADYEGTVYELLSKIDASKLNSNFYKTELLKPLGIIDLYDREVNELSGGELQRVAIAATLLRDADIYLLDEPSAYLDVEQRLAVSRAIRHLMEKNEKTALVVEHDVLMIDYVSDRLMVFEGEPGKYGRALPPMGMREGMNRFLASIGITFRRDPDTGRPRANKEGSVKDREQKEKGEYYYIA 590
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ABC_tran-1yqtA01 A:378-482                                                                               ------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ABC_tran-1yqtA02 A:378-482                                                                               ------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ...eeee......eee.........eeeee.....hhhhhhhhhh............hhhhhhhhh...hhhhhhhhhhh.....eee..hhhhhhhhh..hhhhhhhhhh...hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhh.eeeeeeee...eeee...eehhhhhhhhhhhee....ee...........hhhhh....eeeee..eeeee..eeeee..eeee...eeeee.....hhhhhhhhhh...............eeee..........hhhhhhhhhhhhhhhhhhhhhhh.....hhhhh..hhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhh.eeeeeeee...eeee...eehhhhhhhhhhh....eee......eee....hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yqt A  76 EEDCVHRYGVNAFVLYRLPVVKEGmVVGIVGPNGTGKSTAVKILAGQLIPNLCGDNDSWDGVIRAFRGNELQNYFEKLKNGEIRPVVKPQYVDLIPKAVKGKVIELLKKADETGKLEEVVKALELENVLEREIQHLSGGELQRVAIAAALLRNATFYFFDEPSSYLDIRQRLNAARAIRRLSEEGKSVLVVEHDLAVLDYLSDIIHVVYGEPGVYGIFSQPKGTRNGINEFLRGYLKDENVRFRPYEIKFTKTGERVEIERETLVTYPRLVKDYGSFRLEVEPGEIKKGEVIGIVGPNGIGKTTFVKmLAGVEEPTEGKIEWDLTVAYKPQYIKADYEGTVYELLSKIDASKLNSNFYKTELLKPLGIIDLYDREVNELSGGELQRVAIAATLLRDADIYLLDEPSAYLDVEQRLAVSRAIRHLmEKNEKTALVVEHDVLmIDYVSDRLmVFEGEPGKYGRALPPmGmREGmNRFLASIGITFRRDPDTGRPRANKEGSVKDREQKEKGEYYYIA 590
                                    85        95    |  105       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       395       405       415       425       435       445       455       465       475       485       495    |  505       515|      525       535     | 545 |     555       565       575       585     
                                                  100-MSE                                                                                                                                                                                                                                                                                    383-MSE                                                                                                              500-MSE         516-MSE  525-MSE         541-MSE |                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             543-MSE                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 547-MSE
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  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 1YQT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YQT)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8U306_PYRFU | Q8U306)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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