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(-) Description

Title :  PFV INTASOME WITH INHIBITOR XZ-115
 
Authors :  S. Hare, P. Cherepanov
Date :  08 Oct 12  (Deposition) - 31 Oct 12  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.68
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Transferase-Dna Complex, Dna Integration, Endonuclease, Metal-Binding, Multifunctional Enzyme, Nuclease, Nucleotidyltransferase, Nucleus, Transferase, Viral Nucleoprotein, Virion, Dna-Binding, Zinc Binding, Hhcc Motif, Viral Protein, Recombination, Inhibitor, Recombination-Inhibitor-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Metifiot, K. Maddali, B. C. Johnson, S. Hare, S. J. Smith, X. Z. Zhao, C. Marchand, T. R. Burke, S. H. Hughes, P. Cherepanov, Y. Pommier
Activities, Crystal Structures And Molecular Dynamics Of Dihydro-1H-Isoindole Derivatives, Inhibitors Of Hiv-1 Integrase.
Acs Chem. Biol. V. 8 209 2013
PubMed-ID: 23075516  |  Reference-DOI: 10.1021/CB300471N

(-) Compounds

Molecule 1 - PFV INTEGRASE
    ChainsA, B
    EC Number2.7.7.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificHUMAN SPUMARETROVIRUS
    Organism Taxid11963
    SynonymINTEGRASE, IN, P42IN
 
Molecule 2 - 19 NUCLEOTIDE PREPROCESSED PFV DONOR DNA (NON-TRANSFERRED STRAND)
    ChainsC
    Organism ScientificHUMAN SPUMARETROVIRUS
    Organism Taxid11963
    Synonym5' UTR
    SyntheticYES
 
Molecule 3 - 17 NUCLEOTIDE PREPROCESSED PFV DONOR DNA (TRANSFERRED STRAND)
    ChainsD
    Organism ScientificHUMAN SPUMARETROVIRUS
    Organism Taxid11963
    Synonym5' UTR
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (2x)ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric Unit (5, 12)
No.NameCountTypeFull Name
1BF31Ligand/Ion2-(3-CHLORO-2-FLUOROBENZYL)-4,5-DIHYDROXY-1H-ISOINDOLE-1,3(2H)-DIONE
2GOL5Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
4SO43Ligand/IonSULFATE ION
5ZN1Ligand/IonZINC ION
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1BF32Ligand/Ion2-(3-CHLORO-2-FLUOROBENZYL)-4,5-DIHYDROXY-1H-ISOINDOLE-1,3(2H)-DIONE
2GOL10Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4SO46Ligand/IonSULFATE ION
5ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:62 , HIS A:66 , CYS A:96 , CYS A:99BINDING SITE FOR RESIDUE ZN A 393
02AC2SOFTWARELYS B:219 , ARG B:222 , SER B:258 , PRO B:259 , VAL B:260BINDING SITE FOR RESIDUE SO4 B1300
03AC3SOFTWAREHIS A:338 , LYS A:339 , HIS A:357 , HOH A:2147BINDING SITE FOR RESIDUE SO4 A1376
04AC4SOFTWARESER A:162 , THR A:163 , SER A:164BINDING SITE FOR RESIDUE GOL A1377
05AC5SOFTWARESER A:136 , GLN A:137 , LYS A:241BINDING SITE FOR RESIDUE GOL A1378
06AC6SOFTWARELEU A:292 , GLN A:296 , TYR B:263 , ASP B:273BINDING SITE FOR RESIDUE GOL B1301
07AC7SOFTWAREGLN A:60 , LEU A:79 , TYR A:80 , PRO A:277 , PHE A:278BINDING SITE FOR RESIDUE GOL A1379
08AC8SOFTWAREASP A:128 , ASP A:185 , BF3 A:1382 , HOH A:2046 , HOH A:2047BINDING SITE FOR RESIDUE MG A1380
09AC9SOFTWAREASP A:128 , GLU A:221 , BF3 A:1382 , HOH A:2048BINDING SITE FOR RESIDUE MG A1381
10BC1SOFTWAREASP A:128 , ASP A:185 , PRO A:214 , GLN A:215 , GLU A:221 , MG A:1380 , MG A:1381 , SO4 A:1383 , HOH A:2047 , HOH A:2048 , DG C:4 , DC D:16 , DA D:17BINDING SITE FOR RESIDUE BF3 A1382
11BC2SOFTWAREGLN A:186 , PRO A:211 , TYR A:212 , BF3 A:1382BINDING SITE FOR RESIDUE SO4 A1383
12BC3SOFTWAREPRO A:115 , ASP A:116 , DT C:3BINDING SITE FOR RESIDUE GOL A1384

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BE0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:131 -Pro A:132
2Gly B:131 -Pro B:132

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BE0)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTEGRASEPS50994 Integrase catalytic domain profile.POL_FOAMV868-1024
 
  2A:117-273
B:117-273
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTEGRASEPS50994 Integrase catalytic domain profile.POL_FOAMV868-1024
 
  4A:117-273
B:117-273

(-) Exons   (0, 0)

(no "Exon" information available for 4BE0)

(-) 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:368
 aligned with POL_FOAMV | P14350 from UniProtKB/Swiss-Prot  Length:1143

    Alignment length:368
                                   768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118        
           POL_FOAMV    759 LDAELDQLLQGHYIKGYPKQYTYFLEDGKVKVSRPEGVKIIPPQSDRQKIVLQAHNLAHTGREATLLKIANLYWWPNMRKDVVKQLGRCQQCLITNASNKASGPILRPDRPQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSATVKSLNVLTSIAIPKVIHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSGSKVERKNSDIKRLLTKLLVGRPTKWYDLLPVVQLALNNTYSPVLKYTPHQLLFGIDSNTPFANQDTLDLTREEELSLLQEIRTSLYHPSTPPASSRSWSPVVGQLVQERVARPASLRPRWHKPSTVLKVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ 1126
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh..............ee..eeeeee..eeee..hhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhh....ee..............eeeeeee..........eeeeeee.....eeeeee...hhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh........hhhhhhhh...............hhhhhhhhhhhhhhh............ee......eeee...............eeeeeeee..eeeee.....eeeee...eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------INTEGRASE  PDB: A:117-273 UniProt: 868-1024                                                                                                                  ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4be0 A    8 LDAELDQLLQGHYIKGYPKQYTYFLEDGKVKVSRPEGVKIIPPQSDRQKIVLQAHNLAHTGREATLLKIANLYWWPNMRKDVVKQLGRCQQCLITNASNKASGPILRPDRPQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSATVKSLNVLTSIAIPKVIHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKRLLTKLLVGRPTKWYDLLPVVQLALNNTYSPVLKYTPHQLLFGIDSNTPFANQDTLDLTREEELSLLQEIRTSLYHPSTPPASSRSWSPVVGQLVQERVARPASLRPRWHKPSTVLKVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ  375
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367        

Chain B from PDB  Type:PROTEIN  Length:184
 aligned with POL_FOAMV | P14350 from UniProtKB/Swiss-Prot  Length:1143

    Alignment length:184
                                   876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046    
           POL_FOAMV    867 DRPQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSATVKSLNVLTSIAIPKVIHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSGSKVERKNSDIKRLLTKLLVGRPTKWYDLLPVVQLALNNTYSPVLKYTPHQLLFGIDSNTPFANQDTLDLTREEELSLLQEIR 1050
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeee..........eeeeeee.....eeeeee...hhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh........hhhhhhhh...............hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -INTEGRASE  PDB: B:117-273 UniProt: 868-1024                                                                                                                  -------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4be0 B  116 DRPQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSATVKSLNVLTSIAIPKVIHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKRLLTKLLVGRPTKWYDLLPVVQLALNNTYSPVLKYTPHQLLFGIDSNTPFANQDTLDLTREEELSLLQEIR  299
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295    

Chain C from PDB  Type:DNA  Length:19
                                                    
                4be0 C    1 ATTGTCATGGAATTTCGCA   19
                                    10         

Chain D from PDB  Type:DNA  Length:17
                                                  
                4be0 D    1 TGCGAAATTCCATGACA   17
                                    10       

   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 4BE0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BE0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BE0)

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (POL_FOAMV | P14350)
molecular function
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004523    RNA-DNA hybrid ribonuclease activity    Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
    GO:0003964    RNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0015074    DNA integration    The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006278    RNA-dependent DNA biosynthetic process    A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.
    GO:0075713    establishment of integrated proviral latency    A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0075732    viral penetration into host nucleus    The crossing by the virus of the host nuclear membrane, either as naked viral genome or for small viruses as an intact capsid.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        POL_FOAMV | P143502lsn 2x6n 2x6s 2x74 2x78 3dlr 3l2q 3l2r 3l2u 3l2v 3l2w 3os0 3os1 3os2 3oy9 3oya 3oyb 3oyc 3oyd 3oye 3oyf 3oyg 3oyh 3oyi 3oyj 3oyk 3oyl 3oym 3oyn 3s3m 3s3n 3s3o 4bac 4bdy 4bdz 4be1 4be2 4e7h 4e7i 4e7j 4e7k 4e7l 4ikf 4ztf 4ztj 5frm 5frn 5fro 5uop 5uoq

(-) Related Entries Specified in the PDB File

2x6n HUMAN FOAMY VIRUS INTEGRASE - CATALYTIC CORE. MANGANESE- BOUND STRUCTURE.
2x6s HUMAN FOAMY VIRUS INTEGRASE - CATALYTIC CORE. MAGNESIUM- BOUND STRUCTURE.
2x74 HUMAN FOAMY VIRUS INTEGRASE - CATALYTIC CORE.
2x78 HUMAN FOAMY VIRUS INTEGRASE - CATALYTIC CORE.
4bac PROTOTYPE FOAMY VIRUS STRAND TRANSFER COMPLEXES ON PRODUCT DNA
4bdy PFV INTASOME WITH INHIBITOR XZ-89
4bdz PFV INTASOME WITH INHIBITOR XZ-90
4be1 PFV INTASOME WITH INHIBITOR XZ-116
4be2 PFV INTASOME WITH INHIBITOR XZ-259