Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF CYTOMEGALOVIRUS UL44 BOUND TO C-TERMINAL PEPTIDE FROM CMV UL54
 
Authors :  B. A. Appleton, J. Brooks, A Loregian, D. J. Filman, D. M. Coen, J. M. Hog
Date :  25 Feb 05  (Deposition) - 27 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Processivity Fold (Same Fold As Hsv Ul42, Pcna, And Homotrimeric Sliding Clamps), Replication-Transferase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. A. Appleton, J. Brooks, A. Loregian, D. J. Filman, D. M. Coen, J. M. Hogle
Crystal Structure Of The Cytomegalovirus Dna Polymerase Subunit Ul44 In Complex With The C Terminus From The Catalytic Subunit. Differences In Structure And Function Relative To Unliganded Ul44.
J. Biol. Chem. V. 281 5224 2006
PubMed-ID: 16371349  |  Reference-DOI: 10.1074/JBC.M506900200
(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
    Fragment: N-TERMINAL DOMAIN
    Gene: UL44
    Organism Common: HUMAN CYTOMEGALOVIRUS
    Organism Scientific: HUMAN HERPESVIRUS 5
    Organism Taxid: 10359
    Synonym: POLYMERASE ACCESSORY PROTEIN, PAP, ICP36 PROTEIN
 
Molecule 2 - DNA POLYMERASE
    Chains: B
    EC Number: 2.7.7.7
    Engineered: YES
    Fragment: C-TERMINAL 22 RESIDUES
    Synonym: POL
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2SO48Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:119 , ASN A:141 , HIS A:145 , HIS A:212 , ARG A:243BINDING SITE FOR RESIDUE SO4 A 701
2AC2SOFTWAREARG A:54 , SER A:55 , HIS A:56 , GLN A:222 , ASN A:225 , HOH A:416BINDING SITE FOR RESIDUE SO4 A 702
3AC3SOFTWAREVAL A:130 , HIS A:131 , GLY A:132 , HIS B:1239BINDING SITE FOR RESIDUE SO4 B 703
4AC4SOFTWAREARG A:257 , ARG B:1224BINDING SITE FOR RESIDUE SO4 B 704
5AC5SOFTWAREGLU A:138 , TYR A:253 , ALA A:255 , HOH A:414BINDING SITE FOR RESIDUE EDO A 801
6AC6SOFTWARELYS A:21BINDING SITE FOR RESIDUE EDO A 802
7AC7SOFTWAREASN A:81 , THR A:84 , SER A:127 , ALA A:128 , HOH A:442BINDING SITE FOR RESIDUE EDO A 803

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:45 -Pro A:46
2Gly A:187 -Pro A:188

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YYP)

(-) 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:249
 aligned with VPAP_HCMVA | P16790 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:263
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268   
          VPAP_HCMVA      9 EPPTLALRLKPYKTAIQQLRSVIRALKENTTVTFLPTPSLILQTVRSHCVSKITFNSSCLYITDKSFQPKTINNSTPLLGNFMYLTSSKDLTKFYVQDISDLSAKISMCAPDFNMEFSSACVHGQDIVRESENSAVHVDLDFGVVADLLKWIGPHTRVKRNVKKAPCPTGTVQILVHAGPPAIKFILTNGSELEFTANNRVSFHGVKNMRINVQLKNFYQTLLNCAVTKLPCTLRIVTEHDTLLYVASRNGLFAVENFLTEEP  271
               SCOP domains d1yypa1 A:9-135 UL44                                                                                                           d1yypa2 A:136-271 UL44                                                                                                                   SCOP domains
               CATH domains 1yypA00 A:9-271  [code=3.70.10.10, no name defined]                                                                                                                                                                                                                     CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------Herpes_PAP-1yypA01 A:116-271                                                                                                                                 Pfam domains
         Sec.struct. author ...eeeehhhhhhhhhhhhhhhhhh....eeeeee...eeeeeeee..eeeeeee....eee.......eeee.ee...eehhhhh......eeeee.....eeeeeeee..eeeeeeee.....eee.......eeeeehhhhhhhhhhhhh.--------------..eeeeeee....eeeeee....eeeee....eeeee...eeeeeehhhhhhhhhhhhh....eeeeee.....eeeeeee...eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yyp A    9 EPPTLALRLKPYKTAIQQLRSVIRALKENTTVTFLPTPSLILQTVRSHCVSKITFNSSCLYITDKSFQPKTINNSTPLLGNFMYLTSSKDLTKFYVQDISDLSAKISMCAPDFNMEFSSACVHGQDIVRESENSAVHVDLDFGVVADLLKWIGP--------------TGTVQILVHAGPPAIKFILTNGSELEFTSNNRVSFHGVKNMRINVQLKNFYQTLLNCAVTKLPCTLRIVTEHDTLLYVASRNGLFAVENFLTEEP  271
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158   |     -       178       188       198       208       218       228       238       248       258       268   
                                                                                                                                                                                   162            177                                                                                              


Chain B from PDB  Type:PROTEIN  Length:20
 aligned with DPOL_HCMVA | P08546 from UniProtKB/Swiss-Prot  Length:1242

    Alignment length:20
                                  1232      1242
          DPOL_HCMVA   1223 RRLHLEPAFLPYSVKAHECC 1242
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author .....hhhhhh.eee.hhh. Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                1yyp B 1223 RRLHLEPAFLPYSVKAHECC 1242
                                  1232      1242
   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, 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  (15, 19)

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.

Chain B   (DPOL_HCMVA | P08546)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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: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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:187 - Pro A:188   [ RasMol ]  
    Thr A:45 - Pro A:46   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1yyp
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DPOL_HCMVA | P08546
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  VPAP_HCMVA | P16790
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.7.7
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  DPOL_HCMVA | P08546
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  VPAP_HCMVA | P16790
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        VPAP_HCMVA | P16790: 1t6l 5iwd 5ixa

(-) Related Entries Specified in the PDB File

1t6l