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(-) Description

Title :  CRYSTAL STRUCTURE OF Y345F MUTANT OF HUMAN PRIMASE P58 IRON-SULFUR CLUSTER DOMAIN
 
Authors :  L. E. Salay, M. K. Thompson, W. J. Chazin
Date :  17 Feb 16  (Deposition) - 01 Mar 17  (Release) - 08 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Replication, Primase, [4Fe-4S], P58C, 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
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Fragment: IRON-SULFUR CLUSTER DOMAIN (UNP RESIDUES 272-457)
    Gene: PRIM2, PRIM2A
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PRIMASE REGULATORY SUBUNIT, DNA PRIMASE 58 KDA SUBUNIT, P58

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1SF42Ligand/IonIRON/SULFUR CLUSTER
2SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:285 , CYS A:287 , CYS A:367 , CYS A:384 , CYS A:424binding site for residue SF4 A 501
2AC2SOFTWAREARG A:302 , HIS A:303 , ARG A:306 , GLN B:329binding site for residue SO4 A 502
3AC3SOFTWAREPRO B:285 , CYS B:287 , CYS B:367 , CYS B:384 , CYS B:424binding site for residue SF4 B 500

(-) SS Bonds  (1, 1)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5I7M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I7M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I7M)

(-) Exons   (0, 0)

(no "Exon" information available for 5I7M)

(-) Sequences/Alignments

Asymmetric/Biological 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    
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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:167
                                                                                                                                                                                                       
               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) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i7m A 270 PNSLDQIDLLSTKSFPPCMRQLHKALRENHHLRHGGRMQYGLFLKGIGLTLEQALQFWKDKGFSYNIRHSDYTPFSCLKIILSNPPSQGDYHGCPFRHSDPELLKQKLQSYKISPGGISQILDLVKGTHYQVACQKYFEMIHNVDDCGFSLNHPNQFFCESQRILNG 457
                                   279       289       299       309       319       342       352|      370       380       390       400       410       420       430       440       450       
                                                                                    328|       352|                                                                                                
                                                                                     342        361                                                                                                


Chain B from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.eeeee........eeeee......hhhhhhhh..........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhh..........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5i7m B 272 SLDQIDLLSTKSFPPCMRQLHKALRENHHLRHGGRMQYGLFLKGIGLTLEQALQFWKQSYNIRHSFYTPFSCLKIILSNPPSQGDYHGCPFRHSDPELLKQKLQSYKISPGGISQILDLVKGTHYQVACQKYFEMIHNVDDCGFSLNHPNQFFCESQRILNG 457
                                   281       291       301       311       321       347     ||365       375       385       395       405       415       425       435       445       455  
                                                                                   329|    353|                                                                                               
                                                                                    346     362
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 5I7M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I7M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I7M)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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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 5dqo 5exr 5f0q 5f0s

(-) Related Entries Specified in the PDB File

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