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(-) Description

Title :  CRYSTAL STRUCTURE OF Y347F MUTANT OF HUMAN PRIMASE P58 IRON-SULFUR CLUSTER DOMAIN
 
Authors :  L. E. Salay, M. K. Thompson, W. J. Chazin
Date :  15 Sep 15  (Deposition) - 21 Sep 16  (Release) - 08 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Iron-Sulfur Cluster, Dna Priming, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. O'Brien, M. E. Holt, M. K. Thompson, L. E. Salay, A. C. Ehlinger, W. J. Chazin, J. K. Barton
The [4Fe4S] Cluster Of Human Dna Primase Functions As A Redox Switch Using Dna Charge Transport.
Science V. 355 2017
PubMed-ID: 28232525  |  Reference-DOI: 10.1126/SCIENCE.AAG1789

(-) Compounds

Molecule 1 - DNA PRIMASE LARGE SUBUNIT
    Chains: A, B, C, D
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Fragment: P58C DOMAIN (UNP RESIDUES 272-464)
    Gene: PRIM2, PRIM2A
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNA PRIMASE 58 KDA SUBUNIT, P58

 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, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SF44Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SF42Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SF42Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (0, 0)

(no "Site" information available for 5DQO)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DQO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DQO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DQO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DQO)

(-) Exons   (0, 0)

(no "Exon" information available for 5DQO)

(-) 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:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.eeee....eeee......hhhhhhhh..........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dqo A 270 PNSLDQIDLLSTKSFPPCMRQLHKALRENHHLRHGGRMQYGLFLKGIGLTLEQASFNIRHSFYTPFSCLKIILSNPPSQGDYHGCPFRHSDPELLKQKLQSYKISPGGISQILDLVKGTHYQVACQKYFEMIHNVDDCGFSLNHPNQFFCESQRILNG 457
                                   279       289       299       309       319   ||  351 ||    369       379       389       399       409       419       429       439       449        
                                                                               323|    353|                                                                                               
                                                                                346     362                                                                                               


Chain B from PDB  Type:PROTEIN  Length:154
                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...eee...eee......hhhhhh............hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dqo B 272 SLDQIDLLSTKSFPPCMRQLHKALRENHHLRHGGRMQYGLFLKGIGLTLEQSFNIRHSYTPFSCLKIILSNPPSQGDYHGCPFRHSDPELLKQKLQSYKISPGGISQILDLVKGTHYQVACQKYFEMIHNVDDCGFSLNHPNQFFCESQRILNG 457
                                   281       291       301       311       321||     363       373       383       393       403       413       423       433       443       453    
                                                                            322|   352|                                                                                               
                                                                             346    362                                                                                               


Chain C from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..eeee.......eeee......hhhhhh............hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dqo C 272 SLDQIDLLSTKSFPPCMRQLHKALRENHHLRHGGRMQYGLFLKGIGLTLEQALQYSFNIRHSFYTPFSCLKIILSNPPSQGDYHGCPFRHSDPELLKQKLQSYKISPGGISQILDLVKGTHYQVACQKYFEMIHNVDDCGFSLNHPNQFFCESQRILN 456
                                   281       291       301       311       321   ||  350  ||   368       378       388       398       408       418       428       438       448        
                                                                               325|     353|                                                                                              
                                                                                345      362                                                                                              


Chain D from PDB  Type:PROTEIN  Length:159
                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.eeeee......eeeee.....hhhhhhhh..........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dqo D 272 SLDQIDLLSTKSFPPCMRQLHKALRENHHLRHGGRMQYGLFLKGIGLTLEQALQFWSFNIRHSFTPFSCLKIILSNPPSQGDYHGCPFRHSDPELLKQKLQSYKISPGGISQILDLVKGTHYQVACQKYFEMIHNVDDCGFSLNHPNQFFCESQRILNG 457
                                   281       291       301       311       321     ||349   ||  368       378       388       398       408       418       428       438       448         
                                                                                 327|    353|                                                                                              
                                                                                  346     363
   Legend:   → Mismatch (orange background)
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  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 5DQO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DQO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DQO)

(-) Gene Ontology  (16, 16)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PRI2_HUMAN | P49643: 3l9q 3q36 4bpu 4bpw 4bpx 4rr2 5exr 5f0q 5f0s 5i7m

(-) Related Entries Specified in the PDB File

3l9q