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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN CYTOMEGALOVIRUS DNA POLYMERASE SUBUNIT, UL44
 
Authors :  B. A. Appleton, A. Loregian, D. J. Filman, D. M. Coen, J. M. Hogle
Date :  06 May 04  (Deposition) - 10 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Processivity Fold, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. A. Appleton, A. Loregian, D. J. Filman, D. M. Coen, J. M. Hogle
The Cytomegalovirus Dna Polymerase Subunit Ul44 Forms A C Clamp-Shaped Dimer.
Mol. Cell V. 15 233 2004
PubMed-ID: 15260974  |  Reference-DOI: 10.1016/J.MOLCEL.2004.06.018
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA POLYMERASE PROCESSIVITY FACTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST15
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: UL44
    Organism Common: HUMAN CYTOMEGALOVIRUS
    Organism Scientific: HUMAN HERPESVIRUS 5
    Organism Taxid: 10359
    Synonym: POLYMERASE ACCESSORY PROTEIN, PAP, ICP36 PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1T6L)

(-) Sites  (0, 0)

(no "Site" information available for 1T6L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T6L)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:45 -Pro A:46

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T6L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T6L)

(-) Exons   (0, 0)

(no "Exon" information available for 1T6L)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:249
 aligned with VPAP_HCMVA | P16790 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:261
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269 
           VPAP_HCMVA    10 PPTLALRLKPYKTAIQQLRSVIRALKENTTVTFLPTPSLILQTVRSHCVSKITFNSSCLYITDKSFQPKTINNSTPLLGNFMYLTSSKDLTKFYVQDISDLSAKISMCAPDFNMEFSSACVHGQDIVRESENSAVHVDLDFGVVADLLKWIGPHTRVKRNVKKAPCPTGTVQILVHAGPPAIKFILTNGSELEFTANNRVSFHGVKNMRINVQLKNFYQTLLNCAVTKLPCTLRIVTEHDTLLYVASRNGLFAVENFLTEE 270
               SCOP domains d1t6la1 A:10-135 UL44                                                                                                         d1t6la2 A:136-270 UL44                                                                                                                  SCOP domains
               CATH domains 1t6lA00 A:10-270  [code=3.70.10.10, no name defined]                                                                                                                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------Herpes_PAP-1t6lA01 A:116-270                                                                                                                                Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhhhhhhhhhh.....eeeee...eeeeeeee..eeeeeee....eee.......eeee.ee...eehhhhh......eeeee.....eeeeeeee..eeeeeeee...............eeeeehhhhhhhhhhhhh.------------....eeeeeee....eeeeee....eeee.....eee.....eeeeeehhhhhhhhhhhhhhh..eeeeeee...eeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t6l A  10 PPTLALRLKPYKTAIQQLRSVIRALKENTTVTFLPTPSLILQTVRSHCVSKITFNSSCLYITDKSFQPKTINNSTPLLGNFMYLTSSKDLTKFYVQDISDLSAKISMCAPDFNMEFSSACVHGQDIVRESENSAVHVDLDFGVVADLLKWIGP------------CPTGTVQILVHAGPPAIKFILTNGSELEFTSNNRVSFHGVKNMRINVQLKNFYQTLLNCAVTKLPCTLRIVTEHDTLLYVASRNGLFAVENFLTEE 270
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159  |      -     | 179       189       199       209       219       229       239       249       259       269 
                                                                                                                                                                                  162          175
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  - → Gap (green background, '-', border residues have a numbering label)
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  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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Herpes_PAP] (2)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (VPAP_HCMVA | P16790)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0030337    DNA polymerase processivity factor activity    An enzyme regulator activity that increases the processivity of polymerization by DNA polymerase, by allowing the polymerase to move rapidly along DNA while remaining topologically bound to it.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0039686    bidirectional double-stranded viral DNA replication    A viral DNA replication process where replication occurs in both directions from the starting point. This creates two replication forks, moving in opposite directions.
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.
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.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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    Thr A:45 - Pro A:46   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        VPAP_HCMVA | P16790: 1yyp 5iwd 5ixa

(-) Related Entries Specified in the PDB File

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