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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN POLYMERASE ALPHA-PRIMASE P58 IRON-SULFUR CLUSTER DOMAIN
 
Authors :  S. Vaithiyalingam, B. F. Eichman, W. J. Chazin
Date :  05 Jan 10  (Deposition) - 14 Jul 10  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Pol Alpha, Primase, Dna Replication, Polymerase, Iron-Sulfur Cluster, Dna-Binding, Dna-Directed Rna Polymerase, Iron, Iron-Sulfur, Metal- Binding, Nucleotidyltransferase, Phosphoprotein, Primosome, Transcription, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Vaithiyalingam, E. M. Warren, B. F. Eichman, W. J. Chazin
Insights Into Eukaryotic Dna Priming From The Structure And Functional Interactions Of The 4Fe-4S Cluster Domain Of Human Dna Primase.
Proc. Natl. Acad. Sci. Usa V. 107 13684 2010
PubMed-ID: 20643958  |  Reference-DOI: 10.1073/PNAS.1002009107

(-) Compounds

Molecule 1 - DNA PRIMASE LARGE SUBUNIT
    ChainsA, B
    EC Number2.7.7.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentIRON-SULFUR CLUSTER DOMAIN (UNP RESIDUES 272-464)
    GenePRIM2, PRIM2A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDNA PRIMASE 58 KDA SUBUNIT, P58

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1SF42Ligand/IonIRON/SULFUR CLUSTER
2SO45Ligand/IonSULFATE ION
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
1SF44Ligand/IonIRON/SULFUR CLUSTER
2SO410Ligand/IonSULFATE ION
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1SF42Ligand/IonIRON/SULFUR CLUSTER
2SO45Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:285 , CYS A:287 , CYS A:367 , CYS A:384 , CYS A:424BINDING SITE FOR RESIDUE SF4 A 500
2AC2SOFTWAREHOH A:37 , THR A:281 , ARG A:289 , LYS A:293 , HOH A:514BINDING SITE FOR RESIDUE SO4 A 502
3AC3SOFTWAREPRO B:285 , CYS B:287 , CYS B:367 , CYS B:384 , CYS B:424 , PRO B:444BINDING SITE FOR RESIDUE SF4 B 500
4AC4SOFTWAREHOH A:196 , ARG A:302 , HIS A:303 , ARG A:306 , GLN B:329 , GLU B:330 , PHE B:331 , HOH B:471BINDING SITE FOR RESIDUE SO4 B 501
5AC5SOFTWAREHOH B:109 , ARG B:289 , LYS B:293 , HOH B:480 , HOH B:502 , HOH B:523BINDING SITE FOR RESIDUE SO4 B 503
6AC6SOFTWAREHOH B:150 , HIS B:300 , ARG B:302 , HIS B:303 , ARG B:306BINDING SITE FOR RESIDUE SO4 B 504
7AC7SOFTWARESER A:346 , LYS B:314 , THR B:319 , ARG B:350 , SER B:352 , PHE B:353BINDING SITE FOR RESIDUE SO4 B 505

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:449 -B:449

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L9Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_059745C287YPRI2_HUMANPolymorphism9476080A/BC287Y
2UniProtVAR_059746D435GPRI2_HUMANPolymorphism4307164A/BD435G
3UniProtVAR_059747Q446HPRI2_HUMANPolymorphism4294007A/BQ446H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_059745C287YPRI2_HUMANPolymorphism9476080A/BC287Y
2UniProtVAR_059746D435GPRI2_HUMANPolymorphism4307164A/BD435G
3UniProtVAR_059747Q446HPRI2_HUMANPolymorphism4294007A/BQ446H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_059745C287YPRI2_HUMANPolymorphism9476080A/BC287Y
2UniProtVAR_059746D435GPRI2_HUMANPolymorphism4307164A/BD435G
3UniProtVAR_059747Q446HPRI2_HUMANPolymorphism4294007A/BQ446H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L9Q)

(-) Exons   (0, 0)

(no "Exon" information available for 3L9Q)

(-) 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:171
 aligned with PRI2_HUMAN | P49643 from UniProtKB/Swiss-Prot  Length:509

    Alignment length:188
                                   279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449        
           PRI2_HUMAN   270 KISLDQIDLLSTKSFPPCMRQLHKALRENHHLRHGGRMQYGLFLKGIGLTLEQALQFWKQEFIKGKMDPDKFDKGYSYNIRHSFGKEGKRTDYTPFSCLKIILSNPPSQGDYHGCPFRHSDPELLKQKLQSYKISPGGISQILDLVKGTHYQVACQKYFEMIHNVDDCGFSLNHPNQFFCESQRILNG 457
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhheeeeeee.....-----------....eeeeeee..------......hhhhhhhh..........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------Y---------------------------------------------------------------------------------------------------------------------------------------------------G----------H----------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l9q A 270 NSSLDQIDLLSTKSFPPCMRQLHKALRENHHLRHGGRMQYGLFLKGIGLTLEQALQFWKQ-----------FDKGYSYNIRHSF------TDYTPFSCLKIILSNPPSQGDYHGCPFRHSDPELLKQKLQSYKISPGGISQILDLVKGTHYQVACQKYFEMIHNVDDCGFSLNHPNQFFCESQRILNG 457
                                   279       289       299       309       319       329         - |     349   |     -|      369       379       389       399       409       419       429       439       449        
                                                                                     329         341         353    360                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:167
 aligned with PRI2_HUMAN | P49643 from UniProtKB/Swiss-Prot  Length:509

    Alignment length:186
                                   281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451      
           PRI2_HUMAN   272 SLDQIDLLSTKSFPPCMRQLHKALRENHHLRHGGRMQYGLFLKGIGLTLEQALQFWKQEFIKGKMDPDKFDKGYSYNIRHSFGKEGKRTDYTPFSCLKIILSNPPSQGDYHGCPFRHSDPELLKQKLQSYKISPGGISQILDLVKGTHYQVACQKYFEMIHNVDDCGFSLNHPNQFFCESQRILNG 457
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) DNA_primase_lrg-3l9qB01 B:272-448                                                                                                                                                --------- Pfam domains (1)
           Pfam domains (2) DNA_primase_lrg-3l9qB02 B:272-448                                                                                                                                                --------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.eeeee.........--------------.eeeee..-----.......hhhhhhhh..........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------Y---------------------------------------------------------------------------------------------------------------------------------------------------G----------H----------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3l9q B 272 SLDQIDLLSTKSFPPCMRQLHKALRENHHLRHGGRMQYGLFLKGIGLTLEQALQFWKQEF--------------SYNIRHSF-----RTDYTPFSCLKIILSNPPSQGDYHGCPFRHSDPELLKQKLQSYKISPGGISQILDLVKGTHYQVACQKYFEMIHNVDDCGFSLNHPNQFFCESQRILNG 457
                                   281       291       301       311       321       331         -    |  351 |     361       371       381       391       401       411       421       431       441       451      
                                                                                     331            346    353   359                                                                                                  

   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 3L9Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L9Q)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PRI2_HUMAN | P49643)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003896    DNA primase activity    Catalysis of the synthesis of a short RNA primer on a DNA template, providing a free 3'-OH that can be extended by DNA-directed DNA polymerases.
    GO:0003899    DNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0006270    DNA replication initiation    The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.
    GO:0006269    DNA replication, synthesis of RNA primer    The synthesis of a short RNA polymer, usually 4-15 nucleotides long, using one strand of unwound DNA as a template; the RNA then serves as a primer from which DNA polymerases extend synthesis.
    GO:0006271    DNA strand elongation involved in DNA replication    The process in which a DNA strand is synthesized from template DNA during replication by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand.
    GO:0000082    G1/S transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
    GO:0000722    telomere maintenance via recombination    Any recombinational process that contributes to the maintenance of proper telomeric length.
cellular component
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:1990077    primosome complex    Any of a family of protein complexes that form at the origin of replication or stalled replication forks and function in replication primer synthesis in all organisms. Early complexes initiate double-stranded DNA unwinding. The core unit consists of a replicative helicase and a primase. The helicase further unwinds the DNA and recruits the polymerase machinery. The primase synthesizes RNA primers that act as templates for complementary stand replication by the polymerase machinery. The primosome contains a number of associated proteins and protein complexes and contributes to the processes of replication initiation, lagging strand elongation, and replication restart.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PRI2_HUMAN | P496433q36 4bpu 4bpw 4bpx 4rr2 5dqo 5exr 5f0q 5f0s 5i7m

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