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(-) Description

Title :  THE STRUCTURE OF THE S. AUREUS DNAG RNA POLYMERASE DOMAIN BOUND TO UTP AND MANGANESE
 
Authors :  R. U. Rymer, F. A. Solorio, C. Chu, J. E. Corn, J. D. Wang, J. M. Berger
Date :  27 Mar 12  (Deposition) - 25 Jul 12  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A
Keywords :  Catalytic Domain, Nucleoside Triphosphate, Nucleoside Polyphosphate, Protein-Ligand Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. U. Rymer, F. A. Solorio, A. K. Tehranchi, C. Chu, J. E. Corn, J. L. Keck J. D. Wang, J. M. Berger
Binding Mechanism Of Metal-Ntp Substrates And Stringent-Response Alarmones To Bacterial Dnag-Type Primases.
Structure V. 20 1478 2012
PubMed-ID: 22795082  |  Reference-DOI: 10.1016/J.STR.2012.05.017

(-) Compounds

Molecule 1 - DNA PRIMASE
    Chains: A
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3) CODON+
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 111-436
    Gene: DNAG
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1BEN3Ligand/IonBENZAMIDINE
2MN3Ligand/IonMANGANESE (II) ION
3UTP1Ligand/IonURIDINE 5'-TRIPHOSPHATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:117 , PHE A:125 , TYR A:128 , VAL A:134 , HOH A:702 , HOH A:734BINDING SITE FOR RESIDUE BEN A 501
2AC2SOFTWAREGLN A:289 , LEU A:290 , SER A:291 , ASP A:292 , LYS A:321 , HIS A:325BINDING SITE FOR RESIDUE BEN A 502
3AC3SOFTWAREGLY A:287 , UTP A:504 , HOH A:796 , HOH A:855BINDING SITE FOR RESIDUE BEN A 503
4AC4SOFTWAREARG A:146 , ARG A:222 , PRO A:229 , LYS A:230 , TYR A:231 , ASN A:233 , GLU A:266 , GLY A:267 , PHE A:268 , ASP A:270 , MET A:286 , GLY A:287 , ASP A:310 , ASP A:343 , BEN A:503 , MN A:506 , MN A:507 , HOH A:618 , HOH A:634 , HOH A:652 , HOH A:738 , HOH A:796 , HOH A:834 , HOH A:930 , HOH A:965BINDING SITE FOR RESIDUE UTP A 504
5AC5SOFTWAREHOH A:623 , HOH A:710 , HOH A:738 , HOH A:789 , HOH A:908 , HOH A:923BINDING SITE FOR RESIDUE MN A 505
6AC6SOFTWAREASP A:310 , ASP A:343 , UTP A:504 , MN A:507 , HOH A:834 , HOH A:932BINDING SITE FOR RESIDUE MN A 506
7AC7SOFTWAREASP A:343 , UTP A:504 , MN A:506 , HOH A:634 , HOH A:930 , HOH A:931BINDING SITE FOR RESIDUE MN A 507

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:228 -Pro A:229

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EDR)

(-) 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    
   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:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..hhhhhhhhh.eee....hhhhhhhhhh..hhhhhhhh..eeee....eeee....eeeeeee.....eeeeeee........eee..............hhhhhhhhhhhhh.eeee.hhhhhhhhhhhh...eee......hhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4edr A 108 SNADDLQMIEMHELIQEFYYYALTKTVEGEQALTYLQERGFTDALIKERGIGFAPDSSHFCHDFLQKKGYDIELAYEAGLLSRNEENFSYYDRFRNRIMFPLKNAQGRIVGYSGRTYTGQEPKYLNSPETPIFQKRKLLYNLDKARKSIRKLDEIVLLEGFMDVIKSDTAGLKNVVATMGTQLSDEHITFIRKLTSNITLMFDGDFAGSEATLKTGQHLLQQGLNVFVIQLPSGMDPDEYIGKYGNDAFTTFVKNDKKSFAHYKVSILKDEIAHNDLSYERYLKELSHDISLMKSSILQQKAINDVAPFFNVSPEQLANEI 428
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427
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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 4EDR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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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
        DNAG_STAAU | O05338: 4e2k 4edg 4edk 4edt 4edv 4ee1

(-) Related Entries Specified in the PDB File

4e2k APO SADNAG RPD
4edg
4edk
4edt
4edv
4ee1