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(-) Description

Title :  CRYSTAL STRUCTURE OF XRN1-SUBSTRATE COMPLEX
 
Authors :  M. Jinek, S. M. Coyle, J. A. Doudna
Date :  18 Dec 10  (Deposition) - 16 Mar 11  (Release) - 03 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase-Dna Complex, Rna Degradation, Exonuclease 5'-3', Rna Interference (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Jinek, S. M. Coyle, J. A. Doudna
Coupled 5' Nucleotide Recognition And Processivity In Xrn1-Mediated Mrna Decay.
Mol. Cell V. 41 600 2011
PubMed-ID: 21362555  |  Reference-DOI: 10.1016/J.MOLCEL.2011.02.004

(-) Compounds

Molecule 1 - LD22664P
    Chains: A
    EC Number: 3.1.13.-
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBAC1
    Expression System Taxid: 7108
    Fragment: RESIDUES 1-1140
    Mutation: YES
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: PACMAN, ISOFORM A, XRN1
 
Molecule 2 - DT11 (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP)-3'
    Chains: B
    Organism Scientific: SYTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:86 , GLU A:177 , HOH A:2002 , HOH A:2003 , HOH A:2004 , HOH A:2005 , HOH A:2006BINDING SITE FOR RESIDUE MG A2141

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y35)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:595 -Pro A:596
2Trp A:697 -Pro A:698

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y35)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y35)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y35)

(-) 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:1026
 aligned with E1JJR3_DROME | E1JJR3 from UniProtKB/TrEMBL  Length:1613

    Alignment length:1140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140
        E1JJR3_DROME      1 MGVPKFFRYISERYPCLSELAREHCIPEFDNLYLDMNGIVHNCSHPDDNNIHFHLEEEQIFQEIFNYVDKLFYLIKPQRLFFLSVDGVAPRAKMNQQRSRRFRTAREAEQQEAKAAQRGELREHERFDSNCITPGTEFMVRLQEGLRAFLKTKISTDPLWQRCTVILSGQEAPGEGEHKIMDYIRYMKTQPDYDPNTRHCLYGLDADLIILGLCTHELHFVVLREEVKFGRNVKRTSVEETRFFLLHLGLLREYLELEFDALRTDEHKLDIAQLIDDWVLMGFLVGNDFIPHLPCLHISSNALPLLYRTYIGIYPTLGGNINENGKLNLRRLQIFISALTEVELDHFKEHADDLKYMNNKSEAFDMDVGEITESQNLDSDLGALINKSMLLYDDDSEEDCSDENAVLLKEFQNYKRNFYRNKFKRDPNDELIEELCHHYVNALQWVLDYYYRGVQSWDWYYPFHYTPFISDLKNIEQVEIAFHMGTPFLPFQQLLAVLPAASAKLLPVAYHDLMLLPTSPLAEFYPLEFESDLNGKKHDWEAVVLIPFIDEGRLLAAMLPCEAQLSLEERERNRHGPMYVYKYSTVAQGPMPAYPPLRALPVLYCTEVAKWSHEIAVNLPYSVCIELPNAARTVFFPGFPTMQHLPFDFELRNDRVKVFEQVSRNQNIVLKPRKRQLEDTLTAVASQYLGKVIHVGWPHLVKAIVVRVATRDQRVDSEGITLNDSRRFDSECKALQEHFINRMGIQFANYDVLVYVRTFAGNSTEFRDKGALMVRDSWSSSVTGYPAQGVVADLTVWERMRKNFLNVEHYFPVGSTIFLITDPYYGSEGTVQDPRLAYTNGRIQVSIMVRPEPKVNAARQLQEERDRDYLSTFQVCNLLRISGRTLGRLSGTVWVVLGPRRQKMENVTKHNIGLQLKYPRQNEERAGYCFRTNNQWYYSSLAVDLMRNYCQRYPDVIDFFGDSNDRAEFVFEQDVFPNAVGHRRVEELANWVRQQPHMKVERISCGSKTVCRETIELLIAAVDDLRSLPVKHVKLQVKPHLLIKPNVTLPDVYRSKRPVRLFDRVVIVRTIYMVPVGTKGTVIGIHPVTDPNPVRLECVHAVDTFCKVLFDSPVPNCNNIHGIAEDRVYKVPEIALVIIK 1140
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains XRN_N-2y35A01 A:1-227                                                                                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------                                                --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------  ----------------------------------      -------------------------------------------------------             -------------------------------------------------------                ----------------------------------------------    ------------------------------------------------------------------------------------            -------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...eeeee........eeeeehhhhhhhhhh.------...hhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh-------...hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhh....eeeeee...........hhhh.eeeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh....ee..eehhhhhhhhhhhhhhhhhhhhhhhh..------------------------------------------------hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh............hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.....................eeeeeehhhhh...............................eeeeee..............eeeeee.......hhhhhhhhhh..eeee.....eeeeeeeeee..eeee..eeee.hhhhhhhhhhhhhhhhhhhhh.......eeeeeee...eeeeee...eeeeee......eeee.hhh.........--....hhhhhh....eeee.hhhhh..eeeeeee.------.eeeee.......hhhhhhhhhhhhhh.eehhhhhhhh..hhhhhhhhhh.....-------------.......ee....eee...eee....eeehhhhhhhhhhhhhhhhhhhhhhhhh.----------------..hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhh----..eeeeehhh.ee....................eeee...........eeee...eeee............eeeeeeeee....------------.eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2y35 A    1 MGVPKFFRYISERYPCLSELAREHCIPEFDNLYLDMNGIVHNCSHP------FHLEEEQIFQEIFNYVDKLFYLIKPQRLFFLSVDGVAPRAKMNQQRSRRFRTAREAEQQEAKAAQR-------RFDSNCITPGTEFMVRLQEGLRAFLKTKISTDPLWQRCTVILSGQEAPGEGEHKIMDYIRYMKTQPDYDPNTRHCLYGLDAALIILGLCTHELHFVVLREEVKFGRNVKRTSVEETRFFLLHLGLLREYLELEFDALRTDEHKLDIAQLIDDWVLMGFLVGNDFIPHLPCLHISSNALPLLYRTYIGIYPTLGGNINENGKLNLRRLQIFISALTEVELDHFKEHADD------------------------------------------------DENAVLLKEFQNYKRNFYRNKFKRDPNDELIEELCHHYVNALQWVLDYYYRGVQSWDWYYPFHYTPFISDLKNIEQVEIAFHMGTPFLPFQQLLAVLPAASAKLLPVAYHDLMLLPTSPLAEFYPLEFESDLNGKKHDWEAVVLIPFIDEGRLLAAMLPCEAQLSLEERERNRHGPMYVYKYSTVAQGPMPAYPPLRALPVLYCTEVAKWSHEIAVNLPYSVCIELPNAARTVFFPGFPTMQHLPFDFELRNDRVKVFEQVSRNQNIVLKPRKRQLEDTLTAVASQYLGKVIHVGWPHLVKAIVVRVATRDQRVDSEGITLNDSRRFDSECKALQEHFINRMGIQFANYDVLVYVRTFAGNSTEFRDKGALMVRDSWSSSVTGYPAQGVVADLTVWER--KNFLNVEHYFPVGSTIFLITDPYYGSEGTVQDPR------RIQVSIMVRPEPKVNAARQLQEERDRDYLSTFQVCNLLRISGRTLGRLSGTVWVV-------------HNIGLQLKYPRQNEERAGYCFRTNNQWYYSSLAVDLMRNYCQRYPDVIDFFGDSN----------------GHRRVEELANWVRQQPHMKVERISCGSKTVCRETIELLIAAVDDLR----KHVKLQVKPHLLIKPNVTLPDVYRSKRPVRLFDRVVIVRTIYMVPVGTKGTVIGIHPVTDPNPVRLECVHAVDTFCKVLFDSPV------------RVYKVPEIALVIIK 1140
                                    10        20        30        40     |   -  |     60        70        80        90       100       110       | -     | 130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350  |      -         -         -         -         - |     410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790        |- |     810       820       830    |    - |     850       860       870       880       890     |   -       910       920       930       940       950       960   |     -         -|      990      1000      1010      1020     |   -|     1040      1050      1060      1070      1080      1090      1100      1110   |     -      1130      1140
                                                                        46     53                                                              118     126                                                                                                                                                                                                                                353                                              402                                                                                                                                                                                                                                                                                                                                                                                                          799  |                              835    842                                                   896           910                                                   964              981                                         1026 1031                                                                               1114         1127             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           802                                                                                                                                                                                                                                                                                                                                                  


Chain A from PDB  Type:PROTEIN  Length:1026
 aligned with Q9VWI1_DROME | Q9VWI1 from UniProtKB/TrEMBL  Length:1612

    Alignment length:1140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140
        Q9VWI1_DROME      1 MGVPKFFRYISERYPCLSELAREHCIPEFDNLYLDMNGIVHNCSHPDDNNIHFHLEEEQIFQEIFNYVDKLFYLIKPQRLFFLSVDGVAPRAKMNQQRSRRFRTAREAEQQEAKAAQRGELREHERFDSNCITPGTEFMVRLQEGLRAFLKTKISTDPLWQRCTVILSGQEAPGEGEHKIMDYIRYMKTQPDYDPNTRHCLYGLDADLIILGLCTHELHFVVLREEVKFGRNVKRTSVEETRFFLLHLGLLREYLELEFDALRTDEHKLDIAQLIDDWVLMGFLVGNDFIPHLPCLHISSNALPLLYRTYIGIYPTLGGNINENGKLNLRRLQIFISALTEVELDHFKEHADDLKYMNNKSEAFDMDVGEITESQNLDSDLGALINKSMLLYDDDSEEDCSDENAVLLKEFQNYKRNFYRNKFKRDPNDELIEELCHHYVNALQWVLDYYYRGVQSWDWYYPFHYTPFISDLKNIEQVEIAFHMGTPFLPFQQLLAVLPAASAKLLPVAYHDLMLLPTSPLAEFYPLEFESDLNGKKHDWEAVVLIPFIDEGRLLAAMLPCEAQLSLEERERNRHGPMYVYKYSTVAQGPMPAYPPLRALPVLYCTEVAKWSHEIAVNLPYSVCIELPNAARTVFFPGFPTMQHLPFDFELRNDRVKVFEQVSRNQNIVLKPRKRQLEDTLTAVASQYLGKVIHVGWPHLVKAIVVRVATRDQRVDSEGITLNDSRRFDSECKALQEHFINRMGIQFANYDVLVYVRTFAGNSTEFRDKGALMVRDSWSSSVTGYPAQGVVADLTVWERMRKNFLNVEHYFPVGSTIFLITDPYYGSEGTVQDPRLAYTNGRIQVSIMVRPEPKVNAARQLQEERDRDYLSTFQVCNLLRISGRTLGRLSGTVWVVLGPRRQKMENVTKHNIGLQLKYPRQNEERAGYCFRTNNQWYYSSLAVDLMRNYCQRYPDVIDFFGDSNDRAEFVFEQDVFPNAVGHRRVEELANWVRQQPHMKVERISCGSKTVCRETIELLIAAVDDLRSLPVKHVKLQVKPHLLIKPNVTLPDVYRSKRPVRLFDRVVIVRTIYMVPVGTKGTVIGIHPVTDPNPVRLECVHAVDTFCKVLFDSPVPNCNNIHGIAEDRVYKVPEIALVIIK 1140
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains XRN_N-2y35A01 A:1-227                                                                                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------                                                --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------  ----------------------------------      -------------------------------------------------------             -------------------------------------------------------                ----------------------------------------------    ------------------------------------------------------------------------------------            -------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...eeeee........eeeeehhhhhhhhhh.------...hhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh-------...hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhh....eeeeee...........hhhh.eeeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh....ee..eehhhhhhhhhhhhhhhhhhhhhhhh..------------------------------------------------hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh............hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.....................eeeeeehhhhh...............................eeeeee..............eeeeee.......hhhhhhhhhh..eeee.....eeeeeeeeee..eeee..eeee.hhhhhhhhhhhhhhhhhhhhh.......eeeeeee...eeeeee...eeeeee......eeee.hhh.........--....hhhhhh....eeee.hhhhh..eeeeeee.------.eeeee.......hhhhhhhhhhhhhh.eehhhhhhhh..hhhhhhhhhh.....-------------.......ee....eee...eee....eeehhhhhhhhhhhhhhhhhhhhhhhhh.----------------..hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhh----..eeeeehhh.ee....................eeee...........eeee...eeee............eeeeeeeee....------------.eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2y35 A    1 MGVPKFFRYISERYPCLSELAREHCIPEFDNLYLDMNGIVHNCSHP------FHLEEEQIFQEIFNYVDKLFYLIKPQRLFFLSVDGVAPRAKMNQQRSRRFRTAREAEQQEAKAAQR-------RFDSNCITPGTEFMVRLQEGLRAFLKTKISTDPLWQRCTVILSGQEAPGEGEHKIMDYIRYMKTQPDYDPNTRHCLYGLDAALIILGLCTHELHFVVLREEVKFGRNVKRTSVEETRFFLLHLGLLREYLELEFDALRTDEHKLDIAQLIDDWVLMGFLVGNDFIPHLPCLHISSNALPLLYRTYIGIYPTLGGNINENGKLNLRRLQIFISALTEVELDHFKEHADD------------------------------------------------DENAVLLKEFQNYKRNFYRNKFKRDPNDELIEELCHHYVNALQWVLDYYYRGVQSWDWYYPFHYTPFISDLKNIEQVEIAFHMGTPFLPFQQLLAVLPAASAKLLPVAYHDLMLLPTSPLAEFYPLEFESDLNGKKHDWEAVVLIPFIDEGRLLAAMLPCEAQLSLEERERNRHGPMYVYKYSTVAQGPMPAYPPLRALPVLYCTEVAKWSHEIAVNLPYSVCIELPNAARTVFFPGFPTMQHLPFDFELRNDRVKVFEQVSRNQNIVLKPRKRQLEDTLTAVASQYLGKVIHVGWPHLVKAIVVRVATRDQRVDSEGITLNDSRRFDSECKALQEHFINRMGIQFANYDVLVYVRTFAGNSTEFRDKGALMVRDSWSSSVTGYPAQGVVADLTVWER--KNFLNVEHYFPVGSTIFLITDPYYGSEGTVQDPR------RIQVSIMVRPEPKVNAARQLQEERDRDYLSTFQVCNLLRISGRTLGRLSGTVWVV-------------HNIGLQLKYPRQNEERAGYCFRTNNQWYYSSLAVDLMRNYCQRYPDVIDFFGDSN----------------GHRRVEELANWVRQQPHMKVERISCGSKTVCRETIELLIAAVDDLR----KHVKLQVKPHLLIKPNVTLPDVYRSKRPVRLFDRVVIVRTIYMVPVGTKGTVIGIHPVTDPNPVRLECVHAVDTFCKVLFDSPV------------RVYKVPEIALVIIK 1140
                                    10        20        30        40     |   -  |     60        70        80        90       100       110       | -     | 130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350  |      -         -         -         -         - |     410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790        |- |     810       820       830    |    - |     850       860       870       880       890     |   -       910       920       930       940       950       960   |     -         -|      990      1000      1010      1020     |   -|     1040      1050      1060      1070      1080      1090      1100      1110   |     -      1130      1140
                                                                        46     53                                                              118     126                                                                                                                                                                                                                                353                                              402                                                                                                                                                                                                                                                                                                                                                                                                          799  |                              835    842                                                   896           910                                                   964              981                                         1026 1031                                                                               1114         1127             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           802                                                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:DNA  Length:4
                                     
                2y35 B    1 TTTT    4
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 2Y35)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y35)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PIN (27)

(-) Gene Ontology  (21, 42)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (E1JJR3_DROME | E1JJR3)
molecular function
    GO:0004534    5'-3' exoribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 5' terminus of an RNA molecule.
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    GO:0006401    RNA catabolic process    The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
    GO:0016246    RNA interference    The process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes.
    GO:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0009267    cellular response to starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nourishment.
    GO:0007391    dorsal closure    The process during Drosophila embryogenesis whereby the ectodermal cells of the lateral epithelium stretch in a coordinated fashion to internalize the amnioserosa cells and close the embryo dorsally.
    GO:0007369    gastrulation    A complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
    GO:0046529    imaginal disc fusion, thorax closure    The joining of the parts of the wing imaginal discs, giving rise to the adult thorax.
    GO:0007476    imaginal disc-derived wing morphogenesis    The process in which the anatomical structures of the imaginal disc-derived wing are generated and organized. The wing is an appendage modified for flying.
    GO:0034428    nuclear-transcribed mRNA catabolic process, exonucleolytic, 5'-3'    The chemical reactions and pathways resulting in the breakdown of the mRNA transcript body that occurs when the 5' end is not protected by a 5'-cap; degradation proceeds in the 5' to 3' direction.
    GO:0000184    nuclear-transcribed mRNA catabolic process, nonsense-mediated decay    The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0010603    regulation of cytoplasmic mRNA processing body assembly    Any process that modulates the rate, frequency, or extent of the aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body.
    GO:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
    GO:0000932    P-body    A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A   (Q9VWI1_DROME | Q9VWI1)
molecular function
    GO:0004534    5'-3' exoribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 5' terminus of an RNA molecule.
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    GO:0006401    RNA catabolic process    The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
    GO:0016246    RNA interference    The process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes.
    GO:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0009267    cellular response to starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nourishment.
    GO:0007391    dorsal closure    The process during Drosophila embryogenesis whereby the ectodermal cells of the lateral epithelium stretch in a coordinated fashion to internalize the amnioserosa cells and close the embryo dorsally.
    GO:0007369    gastrulation    A complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
    GO:0046529    imaginal disc fusion, thorax closure    The joining of the parts of the wing imaginal discs, giving rise to the adult thorax.
    GO:0007476    imaginal disc-derived wing morphogenesis    The process in which the anatomical structures of the imaginal disc-derived wing are generated and organized. The wing is an appendage modified for flying.
    GO:0034428    nuclear-transcribed mRNA catabolic process, exonucleolytic, 5'-3'    The chemical reactions and pathways resulting in the breakdown of the mRNA transcript body that occurs when the 5' end is not protected by a 5'-cap; degradation proceeds in the 5' to 3' direction.
    GO:0000184    nuclear-transcribed mRNA catabolic process, nonsense-mediated decay    The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0010603    regulation of cytoplasmic mRNA processing body assembly    Any process that modulates the rate, frequency, or extent of the aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body.
    GO:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
    GO:0000932    P-body    A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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