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(-) Description

Title :  STRUCTURE OF PYRR PROTEIN FROM BACILLUS SUBTILIS WITH GMP
 
Authors :  T. Perica, Y. Kondo, S. Tiwari, S. Mclaughlin, A. Steward, N. Reuter, J. S. A. Teichmann
Date :  30 Mar 14  (Deposition) - 17 Dec 14  (Release) - 31 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Rna Binding Proteins, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Perica, Y. Kondo, S. P. Tiwari, S. H. Mclaughlin, K. R. Kemplen, X. Zhang, A. Steward, N. Reuter, J. Clarke, S. A. Teichmann
Evolution Of Oligomeric State Through Allosteric Pathways That Mimic Ligand Binding.
Science V. 346 54346 2014
PubMed-ID: 25525255  |  Reference-DOI: 10.1126/SCIENCE.1254346

(-) Compounds

Molecule 1 - BIFUNCTIONAL PROTEIN PYRR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PRSET
    Expression System Taxid: 469008
    Expression System Variant: C41
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: PYRIMIDINE OPERON REGULATORY PROTEIN PYRR

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
15GP6Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2GOL1Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:40 , ASP A:105 , ASP A:106 , VAL A:107 , TYR A:109 , THR A:110 , GLY A:111 , ARG A:112 , THR A:113 , ARG A:138 , LYS A:161 , VAL A:162 , HOH A:309 , HOH A:312 , HOH A:318 , HOH A:327 , HOH C:305binding site for residue 5GP A 201
2AC2SOFTWARETHR A:18 , HIS A:22 , ARG A:53 , ILE A:57 , GLU A:181 , HIS C:22 , ILE C:57binding site for residue GOL A 202
3AC3SOFTWARELYS B:40 , ASP B:105 , ASP B:106 , VAL B:107 , TYR B:109 , THR B:110 , GLY B:111 , ARG B:112 , THR B:113 , ARG B:138 , LYS B:161 , VAL B:162 , HOH B:307 , HOH B:330binding site for residue 5GP B 201
4AC4SOFTWAREHIS B:140 , PRO B:155 , THR B:156 , SER B:157 , HOH B:309 , HOH B:331 , LYS C:4 , ALA C:5 , ILE C:7 , LYS C:152 , PRO C:155 , THR C:156 , GLU C:160 , ILE C:177 , 5GP C:201binding site for residue 5GP B 202
5AC5SOFTWAREILE B:7 , LYS B:152 , PRO B:155 , THR B:156 , GLU B:160 , 5GP B:202 , HOH B:310 , LYS C:4 , HIS C:140 , PRO C:155 , THR C:156 , SER C:157 , GLU C:160 , HOH C:340binding site for residue 5GP C 201
6AC6SOFTWARELYS C:40 , ASP C:105 , ASP C:106 , VAL C:107 , TYR C:109 , THR C:110 , GLY C:111 , ARG C:112 , THR C:113 , ARG C:138 , VAL C:162 , HOH C:318 , HOH C:341 , HOH C:356binding site for residue 5GP C 202
7AC7SOFTWARELYS D:40 , ASP D:105 , ASP D:106 , VAL D:107 , TYR D:109 , THR D:110 , GLY D:111 , ARG D:112 , THR D:113 , ARG D:138 , LYS D:161 , VAL D:162 , HOH D:303 , HOH D:325 , HOH D:328 , HOH D:331binding site for residue 5GP D 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P86)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp D:74 -Asp D:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P86)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P86)

(-) Exons   (0, 0)

(no "Exon" information available for 4P86)

(-) 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:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeee........eeeeeeeee..hhhhhhhhhhhhhhh...eeeeeeeee...........eeeee......eeeeeehhhhhh..eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p86 A   3 QKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGNPVTVGEIDITLYRDDLSTSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYENE 181
                                    12        22        32        42        52        62        72    ||  84        94       104       114       124       134       144       154       164       174       
                                                                                                     77|                                                                                                     
                                                                                                      80                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhh....eeeeeeeee........eeeeeeee........eeeeeeeee..hhhhhhhhhhhh......eeeeeeeee...........eeeee......eeeeeehhhhhh..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p86 B   4 KAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGNPVTVGEIDITLYRDDLTSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYENE 181
                                    13        23        33        43        53        63        73  ||    86        96       106       116       126       136       146       156       166       176     
                                                                                                   76|                                                                                                     
                                                                                                    80                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhh....eeeeeeeee.......eeeeeeee........eeeeeeeee..hhhhhhhhhhhhhhh...eeeeeeeee...........eeeee......eeeeeehhhhhh..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p86 C   3 QKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGNPVTVGEIDITLYRDDLSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYEN 180
                                    12        22        32        42        52        62        72   ||   86        96       106       116       126       136       146       156       166       176    
                                                                                                    76|                                                                                                   
                                                                                                     81                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeeeeeee.......eeeeeeee........eeeeeeeee..hhhhhhhhhhhhhhh...eeeeeeeee...........eeeee......eeeeeehhhhhh..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p86 D   3 QKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGNPVTVGEIDITLYRDDLSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYEN 180
                                    12        22        32        42        52        62        72   ||   86        96       106       116       126       136       146       156       166       176    
                                                                                                    76|                                                                                                   
                                                                                                     81
   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 4P86)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P86)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P86)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4P86)

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  Cis Peptide Bonds
    Asp D:74 - Asp D:75   [ RasMol ]  
 

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