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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC SUBUNIT OF HUMAN PRIMASE BOUND TO UTP AND MN
 
Authors :  S. Vaithiyalingam, B. F. Eichman, W. J. Chazin
Date :  02 Jul 13  (Deposition) - 11 Dec 13  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Prim Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Vaithiyalingam, D. R. Arnett, A. Aggarwal, B. F. Eichman, E. Fanning, W. J. Chazin
Insights Into Eukaryotic Primer Synthesis From Structures O The P48 Subunit Of Human Dna Primase.
J. Mol. Biol. V. 426 558 2014
PubMed-ID: 24239947  |  Reference-DOI: 10.1016/J.JMB.2013.11.007

(-) Compounds

Molecule 1 - DNA PRIMASE SMALL SUBUNIT
    Chains: A
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CATALYTIC SUBUNIT P48, UNP RESIDUES 1-390 (DELTA 360-379)
    Gene: PRIM1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNA PRIMASE 49 KDA SUBUNIT, P49

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
2UTP1Ligand/IonURIDINE 5'-TRIPHOSPHATE
3ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:121 , CYS A:122 , CYS A:128 , CYS A:131BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREASP A:109 , ARG A:163 , HIS A:166 , UTP A:504BINDING SITE FOR RESIDUE MN A 502
3AC3SOFTWAREASP A:109 , UTP A:504 , HOH A:627BINDING SITE FOR RESIDUE MN A 503
4AC4SOFTWAREASP A:109 , SER A:160 , ARG A:162 , ARG A:163 , HIS A:166 , LYS A:318 , HIS A:324 , MN A:502 , MN A:503BINDING SITE FOR RESIDUE UTP A 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LIL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LIL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LIL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LIL)

(-) Exons   (0, 0)

(no "Exon" information available for 4LIL)

(-) Sequences/Alignments

Asymmetric/Biological 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:370
                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.hhhhhhhhhhh.......eeeeee.hhh.eeeee...hhhhhhhhhhhhh..eeeeeeee..hhhhh.........eee..eeeeee.hhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....eeeee....eeeeee...hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh............hhhhhhhhhhhhh...hhhhhhh....ee................hhhhhhhhhhhhh.hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lil A   6 PTELPELLKLYYRRLFPYSQYYRWLNYIKNYFQHREFSFTLKDDIYIRYQSFNNQSDLEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFDIDMTDYDDVRRCCSDICPKCWTLMTMAIRIIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKLSSAVRSGIVEYLSLVKKKKVHLSEKIHPFIRKSINIIKKYFEEYALVNQDILENKESWDKILALVPETIHDELQQSFQKSHNSLQRWEHLKKVASRYQNNIKNDKYGPWLEWEIMLQYCFPRLDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTISFICRELDATRDYKKTSLAPYVKVFEHFLENLDKS 405
                                    15        25      ||38        48        58        68        78        88        98       108       118    || 130       140       150       160       170       180       190  ||   205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355   ||  385       395       405
                                                     32|                                                                                    123|                                                                193|                                                                                                                                                             359|                         
                                                      36                                                                                     126                                                                 199                                                                                                                                                              380
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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 4LIL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LIL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LIL)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  4lil
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  PRI1_HUMAN | P49642
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  2.7.7.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRI1_HUMAN | P49642: 4bpu 4bpw 4bpx 4lik 4mhq 4rr2 5exr

(-) Related Entries Specified in the PDB File

4lik CATALYTIC SUBUNIT OF HUMAN PRIMASE
4lim CATALYTIC SUBUNIT OF HUMAN PRIMASE BOUND TO ZN