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(-) Description

Title :  HUMAN CYTOMEGALOVIRUS TERMINASE NUCLEASE DOMAIN
 
Authors :  M. Nadal, P. J. Mas, A. G. Blanco, C. Arnan, M. Sola, D. J. Hart, M. Coll
Date :  22 May 10  (Deposition) - 06 Oct 10  (Release) - 06 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Terminase, Nuclease, Human Cytomegalovirus, Hcmv, Herpesvirus, Dna Packaging, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Nadal, P. J. Mas, A. G. Blanco, C. Arnan, M. Sola, D. J. Hart, M. Coll
Structure And Inhibition Of Herpesvirus Dna Packaging Terminase Nuclease Domain.
Proc. Natl. Acad. Sci. Usa V. 107 16078 2010
PubMed-ID: 20805464  |  Reference-DOI: 10.1073/PNAS.1007144107

(-) Compounds

Molecule 1 - TERMINASE SUBUNIT UL89 PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 418-674
    Organism Scientific: HUMAN HERPESVIRUS 5
    Organism Taxid: 10363
    Strain: TOWNE

 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  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1MG7Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:439 , GLU A:618 , ASN B:447BINDING SITE FOR RESIDUE MG A 4
2AC2SOFTWAREASP B:463 , GLU B:534BINDING SITE FOR RESIDUE MG B 1
3AC3SOFTWAREASN A:447 , ASP B:439 , GLU B:618BINDING SITE FOR RESIDUE MG B 5
4AC4SOFTWAREASP C:463 , GLU C:534 , ASN C:536 , THR C:537BINDING SITE FOR RESIDUE MG C 2
5AC5SOFTWAREASP C:439 , GLU C:618 , ASN D:447BINDING SITE FOR RESIDUE MG C 7
6AC6SOFTWAREASP D:463 , GLU D:534 , ASN D:536BINDING SITE FOR RESIDUE MG D 3
7AC7SOFTWAREASN C:447 , ASP D:439 , GLU D:618BINDING SITE FOR RESIDUE MG D 6

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N4P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3N4P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N4P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N4P)

(-) Exons   (0, 0)

(no "Exon" information available for 3N4P)

(-) 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:216
 aligned with TRM3_HCMVA | P16732 from UniProtKB/Swiss-Prot  Length:674

    Alignment length:246
                                   438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668      
           TRM3_HCMVA   429 LITDQSREEFDILRYSTLNTNAYDYFGKTLYVYLDPAFTTNRKASGTGVAAVGAYRHQFLIYGLEHFFLRDLSESSEVAIAECAAHMIISVLSLHPYLDELRIAVEGNTNQAAAVRIACLIRQSVQSSTLIRVLFYHTPDQNHIEQPFYLMGRDKALAVEQFISRFNSGYIKASQELVSYTIKLSHDPIEYLLEQIQNLHRVTLAEGTTARYSAKRQNRISDDLIIAVIMATYLCDDIHAIRFRVS 674
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhheee.hhhh........eeeeeee..--------.eeeeeeeee..eeeeeeeeee..---..hhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhhhhhh..eeeee.eee...eee......hhhhhhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhh...-------------------.hhhhhhhhhhhhhhhhhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3n4p A 429 LITDQSREEFDILRYSTLNTNAYDYFGKTLYVYLDPA--------GTGVAAVGAYRHQFLIYGLEHFFL---SESSEVAIAECAAHMIISVLSLHPYLDELRIAVEGNTNQAAAVRIACLIRQSVQSSTLIRVLFYHTPDQNHIEQPFYLMGRDKALAVEQFISRFNSGYIKASQELVSYTIKLSHDPIEYLLEQIQNLHR-------------------SDDLIIAVIMATYLCDDIHAIRFRVS 674
                                   438       448       458      |  -     | 478       488        |-  |    508       518       528       538       548       558       568       578       588       598       608       618       628|        -         -|      658       668      
                                                              465      474                    497 501                                                                                                                             629                 649                         


Chain B from PDB  Type:PROTEIN  Length:227
 aligned with TRM3_HCMVA | P16732 from UniProtKB/Swiss-Prot  Length:674

    Alignment length:246
                                   438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668      
           TRM3_HCMVA   429 LITDQSREEFDILRYSTLNTNAYDYFGKTLYVYLDPAFTTNRKASGTGVAAVGAYRHQFLIYGLEHFFLRDLSESSEVAIAECAAHMIISVLSLHPYLDELRIAVEGNTNQAAAVRIACLIRQSVQSSTLIRVLFYHTPDQNHIEQPFYLMGRDKALAVEQFISRFNSGYIKASQELVSYTIKLSHDPIEYLLEQIQNLHRVTLAEGTTARYSAKRQNRISDDLIIAVIMATYLCDDIHAIRFRVS 674
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhheee.hhhh........eeeeee............eeeeeeeee..eeeeeeeeee..----.hhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhhhhhh..eeeee.ee.....ee......hhhhhhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhh.....---------------....hhhhhhhhhhhhhhhhhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3n4p B 429 LITDQSREEFDILRYSTLNTNAYDYFGKTLYVYLDPAFTTNRKASGTGVAAVGAYRHQFLIYGLEHFFL----ESSEVAIAECAAHMIISVLSLHPYLDELRIAVEGNTNQAAAVRIACLIRQSVQSSTLIRVLFYHTPDQNHIEQPFYLMGRDKALAVEQFISRFNSGYIKASQELVSYTIKLSHDPIEYLLEQIQNLHRV---------------NRISDDLIIAVIMATYLCDDIHAIRFRVS 674
                                   438       448       458       468       478       488        |-   |   508       518       528       538       548       558       568       578       588       598       608       618       628 |       -       648       658       668      
                                                                                              497  502                                                                                                                             630             646                            


Chain C from PDB  Type:PROTEIN  Length:218
 aligned with TRM3_HCMVA | P16732 from UniProtKB/Swiss-Prot  Length:674

    Alignment length:245
                                   438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668     
           TRM3_HCMVA   429 LITDQSREEFDILRYSTLNTNAYDYFGKTLYVYLDPAFTTNRKASGTGVAAVGAYRHQFLIYGLEHFFLRDLSESSEVAIAECAAHMIISVLSLHPYLDELRIAVEGNTNQAAAVRIACLIRQSVQSSTLIRVLFYHTPDQNHIEQPFYLMGRDKALAVEQFISRFNSGYIKASQELVSYTIKLSHDPIEYLLEQIQNLHRVTLAEGTTARYSAKRQNRISDDLIIAVIMATYLCDDIHAIRFRV 673
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhheee.hhhh........eeeeee...------...eeeeeeeee..eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhhhhhh..eeeee.ee.....ee....hhhhhhhhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhh..---------------------.hhhhhhhhhhhhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n4p C 429 LITDQSREEFDILRYSTLNTNAYDYFGKTLYVYLDPA------ASGTGVAAVGAYRHQFLIYGLEHFFLRDLSESSEVAIAECAAHMIISVLSLHPYLDELRIAVEGNTNQAAAVRIACLIRQSVQSSTLIRVLFYHTPDQNHIEQPFYLMGRDKALAVEQFISRFNSGYIKASQELVSYTIKLSHDPIEYLLEQIQNL---------------------SDDLIIAVIMATYLCDDIHAIRFRV 673
                                   438       448       458      |  -   |   478       488       498       508       518       528       538       548       558       568       578       588       598       608       618        |-         -         -|      658       668     
                                                              465    472                                                                                                                                                        627                   649                        


Chain D from PDB  Type:PROTEIN  Length:212
 aligned with TRM3_HCMVA | P16732 from UniProtKB/Swiss-Prot  Length:674

    Alignment length:246
                                   438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668      
           TRM3_HCMVA   429 LITDQSREEFDILRYSTLNTNAYDYFGKTLYVYLDPAFTTNRKASGTGVAAVGAYRHQFLIYGLEHFFLRDLSESSEVAIAECAAHMIISVLSLHPYLDELRIAVEGNTNQAAAVRIACLIRQSVQSSTLIRVLFYHTPDQNHIEQPFYLMGRDKALAVEQFISRFNSGYIKASQELVSYTIKLSHDPIEYLLEQIQNLHRVTLAEGTTARYSAKRQNRISDDLIIAVIMATYLCDDIHAIRFRVS 674
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) DNA_pack_C-3n4pD01 D:429-674                                                                                                                                                                                                                           Pfam domains (1)
           Pfam domains (2) DNA_pack_C-3n4pD02 D:429-674                                                                                                                                                                                                                           Pfam domains (2)
           Pfam domains (3) DNA_pack_C-3n4pD03 D:429-674                                                                                                                                                                                                                           Pfam domains (3)
           Pfam domains (4) DNA_pack_C-3n4pD04 D:429-674                                                                                                                                                                                                                           Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhheee.............eeeeeee..---------.eeeeeeee..eeeeeeeee..-----hhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhhhhhh..eeeee.eee...eee......hhhhhhhhhhhhhhhhh.eeeeeeee........hhhhhhhhhhhh...--------------------hhhhhhhhhhhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3n4p D 429 LITDQSREEFDILRYSTLNTNAYDYFGKTLYVYLDPA---------TGVAAVGAYRHQFLIYGLEHFF-----ESSEVAIAECAAHMIISVLSLHPYLDELRIAVEGNTNQAAAVRIACLIRQSVQSSTLIRVLFYHTPDQNHIEQPFYLMGRDKALAVEQFISRFNSGYIKASQELVSYTIKLSHDPIEYLLEQIQNLHR--------------------DDLIIAVIMATYLCDDIHAIRFRVS 674
                                   438       448       458      |  -      |478       488       | -   |   508       518       528       538       548       558       568       578       588       598       608       618       628|        -         - |     658       668      
                                                              465       475                  496   502                                                                                                                            629                  650
   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 3N4P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N4P)

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (TRM3_HCMVA | P16732)
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.
biological process
    GO:0006323    DNA packaging    Any process in which DNA and associated proteins are formed into a compact, orderly structure.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
    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.

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  3n4p
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRM3_HCMVA | P16732: 3n4q

(-) Related Entries Specified in the PDB File

3n4q