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(-) Description

Title :  CATALYTIC DOMAIN OF BACTERIOPHAGE HP1 INTEGRASE
 
Authors :  A. B. Hickman, S. Waninger, J. J. Scocca, F. Dyda
Date :  17 Apr 97  (Deposition) - 20 Aug 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Dna Integration, Recombination (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. B. Hickman, S. Waninger, J. J. Scocca, F. Dyda
Molecular Organization In Site-Specific Recombination: The Catalytic Domain Of Bacteriophage Hp1 Integrase At 2. 7 A Resolution.
Cell(Cambridge, Mass. ) V. 89 227 1997
PubMed-ID: 9108478  |  Reference-DOI: 10.1016/S0092-8674(00)80202-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HP1 INTEGRASE
    Cell LineHAEMOPHILUS INFLUENZAE L10
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHPC
    Expression System StrainDH5 ALPHA
    Expression System Taxid562
    Expression System VectorPRAD18
    Expression System Vector TypePRLM156
    FragmentCATALYTIC DOMAIN, RESIDUES 168 - 337
    GeneGENBANK U24159
    Organism ScientificHAEMOPHILUS PHAGE HP1
    Organism Taxid10690
    StrainHP1C1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1MG5Ligand/IonMAGNESIUM ION
2SO48Ligand/IonSULFATE ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO45Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO43Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:283 , HIS A:306 , ARG A:314 , TYR A:315BINDING SITE FOR RESIDUE SO4 A 105
02AC2SOFTWAREHIS B:280 , ARG B:283 , HIS B:284 , HIS B:306 , ARG B:314 , TYR B:315BINDING SITE FOR RESIDUE SO4 B 106
03AC3SOFTWAREARG C:207 , HIS C:280 , ARG C:283 , HIS C:306 , ARG C:314 , HOH C:2081BINDING SITE FOR RESIDUE SO4 C 107
04AC4SOFTWAREARG D:283 , HIS D:306 , MET D:311 , ARG D:314BINDING SITE FOR RESIDUE SO4 D 108
05AC5SOFTWARETHR A:215 , GLN A:216 , SER A:217 , ARG A:251 , GLY A:252 , HIS A:317BINDING SITE FOR RESIDUE SO4 A 109
06AC6SOFTWAREGLN B:216 , SER B:217 , ARG B:251 , GLY B:252 , HIS B:317BINDING SITE FOR RESIDUE SO4 B 110
07AC7SOFTWAREARG A:314 , HOH A:2008 , SER D:189 , ARG D:190 , ASN D:191 , SER D:261 , ASN D:264 , ARG D:268BINDING SITE FOR RESIDUE SO4 D 111
08AC8SOFTWARESER A:189 , ARG A:190 , ASN A:264 , HOH A:2024 , ASP C:187 , ASN C:188BINDING SITE FOR RESIDUE SO4 A 112
09AC9SOFTWAREHOH A:2007 , GLU D:260BINDING SITE FOR RESIDUE MG D 102
10ACAUNKNOWNTYR A:315 , ARG A:207 , HIS A:280 , ARG A:283ACTIVE SITE.
11ACBUNKNOWNTYR B:315 , ARG B:207 , HIS B:280 , ARG B:283ACTIVE SITE.
12ACCUNKNOWNTYR C:315 , ARG C:207 , HIS C:280 , ARG C:283ACTIVE SITE.
13ACDUNKNOWNTYR D:315 , ARG D:207 , HIS D:280 , ARG D:283ACTIVE SITE.
14BC1SOFTWAREGLU A:270 , GLU B:270 , HOH B:2065 , GLU C:270BINDING SITE FOR RESIDUE MG C 103
15BC2SOFTWAREGLU C:263BINDING SITE FOR RESIDUE MG C 104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1AIH)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1AIH)

(-) 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:170
 aligned with VINT_BPHC1 | P21442 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:170
                                   177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337
           VINT_BPHC1   168 ETELAFLYERDIYRLLAECDNSRNPDLGLIVRICLATGARWSEAETLTQSQVMPYKITFTNTKSKKNRTVPISKELFDMLPKKRGRLFNDAYESFENAVLRAEIELPKGQLTHVLRHTFASHFMMNGGNILVLKEILGHSTIEMTMRYAHFAPSHLESAVKFNPLSNPAQ 337
               SCOP domains d1aiha_ A: Integrase                                                                                                                                                       SCOP domains
               CATH domains 1aihA00 A:168-337 Intergrase catalytic core                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhh..........eeeee......eeeee..hhhhhh............hhhhhhhhhh............hhhhhhhhhhhh....hhhhhhhh....hhhhhhhhhh....hhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1aih A 168 ETELAFLYERDIYRLLAECDNSRNPDLGLIVRICLATGARWSEAETLTQSQVMPYKITFTNTKSKKNRTVPISDELFDMLPKKRGRLFNDAYESFENAVLRAEIELPKGQLTHVLRHTFASHFMMNGGNILVLKEILGHSTIEMTMRYAHFAPSHLESAVKFNPLSNPAQ 337
                                   177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337

Chain B from PDB  Type:PROTEIN  Length:168
 aligned with VINT_BPHC1 | P21442 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:168
                                   179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329        
           VINT_BPHC1   170 ELAFLYERDIYRLLAECDNSRNPDLGLIVRICLATGARWSEAETLTQSQVMPYKITFTNTKSKKNRTVPISKELFDMLPKKRGRLFNDAYESFENAVLRAEIELPKGQLTHVLRHTFASHFMMNGGNILVLKEILGHSTIEMTMRYAHFAPSHLESAVKFNPLSNPAQ 337
               SCOP domains d1aihb_ B: Integrase                                                                                                                                                     SCOP domains
               CATH domains 1aihB00 B:170-337 Intergrase catalytic core                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhh.......hhhhhhhhhhh...hhhhh...hhh....eeeee......eeeee..hhhhhh............hhhhhhhhhhh........hhhhhhhhhhhhhhh....hhhhhhhh....hhhhhhhhhh....hhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1aih B 170 ELAFLYERDIYRLLAECDNSRNPDLGLIVRICLATGARWSEAETLTQSQVMPYKITFTNTKSKKNRTVPISDELFDMLPKKRGRLFNDAYESFENAVLRAEIELPKGQLTHVLRHTFASHFMMNGGNILVLKEILGHSTIEMTMRYAHFAPSHLESAVKFNPLSNPAQ 337
                                   179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329        

Chain C from PDB  Type:PROTEIN  Length:168
 aligned with VINT_BPHC1 | P21442 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:168
                                   179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329        
           VINT_BPHC1   170 ELAFLYERDIYRLLAECDNSRNPDLGLIVRICLATGARWSEAETLTQSQVMPYKITFTNTKSKKNRTVPISKELFDMLPKKRGRLFNDAYESFENAVLRAEIELPKGQLTHVLRHTFASHFMMNGGNILVLKEILGHSTIEMTMRYAHFAPSHLESAVKFNPLSNPAQ 337
               SCOP domains d1aihc_ C: Integrase                                                                                                                                                     SCOP domains
               CATH domains 1aihC00 C:170-337 Intergrase catalytic core                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh......hhhhhhhhhhh...hhhhh...hhh....eeee........eeee..hhhhhh............hhhhhhhhhh.........hhhhhhhhhhhhhhh....hhhhhhhh....hhhhhhhhhh....hhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1aih C 170 ELAFLYERDIYRLLAECDNSRNPDLGLIVRICLATGARWSEAETLTQSQVMPYKITFTNTKSKKNRTVPISDELFDMLPKKRGRLFNDAYESFENAVLRAEIELPKGQLTHVLRHTFASHFMMNGGNILVLKEILGHSTIEMTMRYAHFAPSHLESAVKFNPLSNPAQ 337
                                   179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329        

Chain D from PDB  Type:PROTEIN  Length:170
 aligned with VINT_BPHC1 | P21442 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:170
                                   177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337
           VINT_BPHC1   168 ETELAFLYERDIYRLLAECDNSRNPDLGLIVRICLATGARWSEAETLTQSQVMPYKITFTNTKSKKNRTVPISKELFDMLPKKRGRLFNDAYESFENAVLRAEIELPKGQLTHVLRHTFASHFMMNGGNILVLKEILGHSTIEMTMRYAHFAPSHLESAVKFNPLSNPAQ 337
               SCOP domains d1aihd_ D: Integrase                                                                                                                                                       SCOP domains
               CATH domains 1aihD00 D:168-337 Intergrase catalytic core                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhh...hhh....eeee........eeee..hhhhhh............hhhhhhhhhh........hhhhhhhhhhhhhhhh....hhhhhhh.....hhhhhhhhhh....hhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1aih D 168 ETELAFLYERDIYRLLAECDNSRNPDLGLIVRICLATGARWSEAETLTQSQVMPYKITFTNTKSKKNRTVPISDELFDMLPKKRGRLFNDAYESFENAVLRAEIELPKGQLTHVLRHTFASHFMMNGGNILVLKEILGHSTIEMTMRYAHFAPSHLESAVKFNPLSNPAQ 337
                                   177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AIH)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (VINT_BPHC1 | P21442)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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: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: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: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.

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