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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PURR COMPLEXED WITH CPRPP
 
Authors :  A. K. Bera, J. Zhu, H. Zalkin, J. L. Smith
Date :  22 Apr 03  (Deposition) - 09 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Bera, J. Zhu, H. Zalkin, J. L. Smith
Functional Dissection Of The Bacillus Subtilis Pur Operator Site.
J. Bacteriol. V. 185 4099 2003
PubMed-ID: 12837784  |  Reference-DOI: 10.1128/JB.185.14.4099-4109.2003

(-) Compounds

Molecule 1 - PUR OPERON REPRESSOR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PURR
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 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
1PCP4Ligand/Ion1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PCP2Ligand/Ion1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1PCP2Ligand/Ion1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:138 , THR A:139 , LYS A:140 , GLY A:178 , ASP A:203 , ASP A:204 , PHE A:205 , LYS A:207 , ALA A:208 , GLY A:209 , GLY A:210 , THR A:211 , HOH A:620 , HOH A:694 , ARG B:160BINDING SITE FOR RESIDUE PCP A 604
2AC2SOFTWAREARG A:160 , VAL B:137 , ALA B:138 , THR B:139 , LYS B:140 , GLY B:141 , LYS B:161 , GLY B:178 , ASP B:203 , ASP B:204 , PHE B:205 , MET B:206 , LYS B:207 , ALA B:208 , GLY B:209 , GLY B:210 , THR B:211 , HOH B:609 , HOH B:610 , HOH B:674 , HOH B:714 , HOH B:760BINDING SITE FOR RESIDUE PCP B 605
3AC3SOFTWAREALA C:138 , THR C:139 , LYS C:140 , LYS C:161 , SER C:177 , GLY C:178 , ASP C:203 , ASP C:204 , PHE C:205 , MET C:206 , LYS C:207 , ALA C:208 , GLY C:209 , GLY C:210 , THR C:211 , HOH C:608 , HOH C:652 , HOH C:659 , HOH C:671 , HOH C:691 , HOH C:745 , ARG D:160 , HOH D:625BINDING SITE FOR RESIDUE PCP C 606
4AC4SOFTWAREARG C:160 , ALA D:138 , THR D:139 , LYS D:140 , SER D:177 , GLY D:178 , ASP D:203 , ASP D:204 , PHE D:205 , MET D:206 , LYS D:207 , ALA D:208 , GLY D:209 , GLY D:210 , THR D:211 , HOH D:619 , HOH D:636 , HOH D:685 , HOH D:725BINDING SITE FOR RESIDUE PCP D 607

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P4A)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:138 -Thr A:139
2Ala B:138 -Thr B:139
3Ala C:138 -Thr C:139
4Ala D:138 -Thr D:139

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P4A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P4A)

(-) Exons   (0, 0)

(no "Exon" information available for 1P4A)

(-) 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:269
 aligned with PURR_BACSU | P37551 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271     
           PURR_BACSU     2 KFRRSGRLVDLTNYLLTHPHELIPLTFFSERYESAKSSISEDLTIIKQTFEQQGIGTLLTVPGAAGGVKYIPKMKQAEAEEFVQTLGQSLANPERILPGGYVYLTDILGKPSVLSKVGKLFASVFAEREIDVVMTVATKGIPLAYAAASYLNVPVVIVRKDNKVTEGSTVSINYVSGSSNRIQTMSLAKRSMKTGSNVLIIDDFMKAGGTINGMINLLDEFNANVAGIGVLVEAEGVDERLVDEYMSLLTLSTINMKEKSIEIQNGNFLRFFKDN 276
               SCOP domains d1p4aa1 A:2-74 N-terminal domain of Bacillus PurR                        d1p4aa2 A:75-276 Pur operon repressor (PurR), C-terminal domain                                                                                                                                            SCOP domains
               CATH domains 1p4aA01 A:2-73 'winged helix' repressor DNA binding domain              1p4aA02 A:74-276  [code=3.40.50.2020, no name defined]                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.....eehhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeee.....eeeeee..hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhh..eeee...------.eeeeeee......eeeeeee.hhh....eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeeee...........eeeeee...........eee.hhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p4a A   2 KFRRSGRLVDLTNYLLTHPHELIPLTFFSERYESAKSSISEDLTIIKQTFEQQGIGTLLTVPGAAGGVKYIPKMKQAEAEEFVQTLGQSLANPERILPGGYVYLTDILGKPSVLSKVGKLFASVFAEREIDVVMTVATKGIPLAYAAASYLNVPVVIVRKD------STVSINYVSGSSNRIQTMSLAKRSMKTGSNVLIIDDFMKAGGTINGMINLLDEFNANVAGIGVLVEAEGVDERLVDEYMSLLTLSTINMKEKSIEIQNGNFLRFFKDN 276
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161|      171       181       191       201       211       221       231       241       251       261       271     
                                                                                                                                                                                          162    169                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:268
 aligned with PURR_BACSU | P37551 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:272
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271  
           PURR_BACSU     2 KFRRSGRLVDLTNYLLTHPHELIPLTFFSERYESAKSSISEDLTIIKQTFEQQGIGTLLTVPGAAGGVKYIPKMKQAEAEEFVQTLGQSLANPERILPGGYVYLTDILGKPSVLSKVGKLFASVFAEREIDVVMTVATKGIPLAYAAASYLNVPVVIVRKDNKVTEGSTVSINYVSGSSNRIQTMSLAKRSMKTGSNVLIIDDFMKAGGTINGMINLLDEFNANVAGIGVLVEAEGVDERLVDEYMSLLTLSTINMKEKSIEIQNGNFLRFF 273
               SCOP domains d1p4ab1 B:2-74 N-terminal domain of Bacillus PurR                        d1p4ab2 B:75-273 Pur operon repressor (PurR), C-terminal domain                                                                                                                                         SCOP domains
               CATH domains 1p4aB01 B:2-73 'winged helix' repressor DNA binding domain              1p4aB02 B:74-273  [code=3.40.50.2020, no name defined]                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh....eehhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeee.....eeeeee..hhhhhhhhhhhhhhhhhhhh.ee...ee.hhhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhh..eeee...----...eeeeeeee..eeeeeeeeee.hhh....eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeeee...........eeeeeeeeee....eeeeee.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p4a B   2 KFRRSGRLVDLTNYLLTHPHELIPLTFFSERYESAKSSISEDLTIIKQTFEQQGIGTLLTVPGAAGGVKYIPKMKQAEAEEFVQTLGQSLANPERILPGGYVYLTDILGKPSVLSKVGKLFASVFAEREIDVVMTVATKGIPLAYAAASYLNVPVVIVRKD----EGSTVSINYVSGSSNRIQTMSLAKRSMKTGSNVLIIDDFMKAGGTINGMINLLDEFNANVAGIGVLVEAEGVDERLVDEYMSLLTLSTINMKEKSIEIQNGNFLRFF 273
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161|    | 171       181       191       201       211       221       231       241       251       261       271  
                                                                                                                                                                                          162  167                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:269
 aligned with PURR_BACSU | P37551 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:272
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271  
           PURR_BACSU     2 KFRRSGRLVDLTNYLLTHPHELIPLTFFSERYESAKSSISEDLTIIKQTFEQQGIGTLLTVPGAAGGVKYIPKMKQAEAEEFVQTLGQSLANPERILPGGYVYLTDILGKPSVLSKVGKLFASVFAEREIDVVMTVATKGIPLAYAAASYLNVPVVIVRKDNKVTEGSTVSINYVSGSSNRIQTMSLAKRSMKTGSNVLIIDDFMKAGGTINGMINLLDEFNANVAGIGVLVEAEGVDERLVDEYMSLLTLSTINMKEKSIEIQNGNFLRFF 273
               SCOP domains d1p4ac1 C:2-74 N-terminal domain of Bacillus PurR                        d1p4ac2 C:75-273 Pur operon repressor (PurR), C-terminal domain                                                                                                                                         SCOP domains
               CATH domains 1p4aC01 C:2-73 'winged helix' repressor DNA binding domain              1p4aC02 C:74-273  [code=3.40.50.2020, no name defined]                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh....eehhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeee.....eeeeee..hhhhhhhhhhhhhhhhhhhh.ee...ee...hhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhh..eeee....---...eeeeee........eeeeee.hhh....eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeeee...........eeeeee...........eee.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p4a C   2 KFRRSGRLVDLTNYLLTHPHELIPLTFFSERYESAKSSISEDLTIIKQTFEQQGIGTLLTVPGAAGGVKYIPKMKQAEAEEFVQTLGQSLANPERILPGGYVYLTDILGKPSVLSKVGKLFASVFAEREIDVVMTVATKGIPLAYAAASYLNVPVVIVRKDN---EGSTVSINYVSGSSNRIQTMSLAKRSMKTGSNVLIIDDFMKAGGTINGMINLLDEFNANVAGIGVLVEAEGVDERLVDEYMSLLTLSTINMKEKSIEIQNGNFLRFF 273
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 |   | 171       181       191       201       211       221       231       241       251       261       271  
                                                                                                                                                                                           163 167                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:268
 aligned with PURR_BACSU | P37551 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:272
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271  
           PURR_BACSU     2 KFRRSGRLVDLTNYLLTHPHELIPLTFFSERYESAKSSISEDLTIIKQTFEQQGIGTLLTVPGAAGGVKYIPKMKQAEAEEFVQTLGQSLANPERILPGGYVYLTDILGKPSVLSKVGKLFASVFAEREIDVVMTVATKGIPLAYAAASYLNVPVVIVRKDNKVTEGSTVSINYVSGSSNRIQTMSLAKRSMKTGSNVLIIDDFMKAGGTINGMINLLDEFNANVAGIGVLVEAEGVDERLVDEYMSLLTLSTINMKEKSIEIQNGNFLRFF 273
               SCOP domains d1p4ad1 D:2-74 N-terminal domain of Bacillus PurR                        d1p4ad2 D:75-273 Pur operon repressor (PurR), C-terminal domain                                                                                                                                         SCOP domains
               CATH domains 1p4aD01 D:2-73 'winged helix' repressor DNA binding domain              1p4aD02 D:74-273  [code=3.40.50.2020, no name defined]                                                                                                                                                   CATH domains
           Pfam domains (1) --PuR_N-1p4aD01 D:4-73                                                  --------------------------------Pribosyltran-1p4aD05 D:106-233                                                                                                  ---------------------------------------- Pfam domains (1)
           Pfam domains (2) --PuR_N-1p4aD02 D:4-73                                                  --------------------------------Pribosyltran-1p4aD06 D:106-233                                                                                                  ---------------------------------------- Pfam domains (2)
           Pfam domains (3) --PuR_N-1p4aD03 D:4-73                                                  --------------------------------Pribosyltran-1p4aD07 D:106-233                                                                                                  ---------------------------------------- Pfam domains (3)
           Pfam domains (4) --PuR_N-1p4aD04 D:4-73                                                  --------------------------------Pribosyltran-1p4aD08 D:106-233                                                                                                  ---------------------------------------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhh.....eehhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeee.....eeeeee..hhhhhhhhhhhhhhhhhhhh.ee...ee...hhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhh..eeee...----...eeeeeee......eeeeeee.hhh....eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeeee...........eeeeee...........eee.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p4a D   2 KFRRSGRLVDLTNYLLTHPHELIPLTFFSERYESAKSSISEDLTIIKQTFEQQGIGTLLTVPGAAGGVKYIPKMKQAEAEEFVQTLGQSLANPERILPGGYVYLTDILGKPSVLSKVGKLFASVFAEREIDVVMTVATKGIPLAYAAASYLNVPVVIVRKD----EGSTVSINYVSGSSNRIQTMSLAKRSMKTGSNVLIIDDFMKAGGTINGMINLLDEFNANVAGIGVLVEAEGVDERLVDEYMSLLTLSTINMKEKSIEIQNGNFLRFF 273
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161|    | 171       181       191       201       211       221       231       241       251       261       271  
                                                                                                                                                                                          162  167
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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  (2, 8)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: HTH (544)
(-)
Clan: PRTase-like (59)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PURR_BACSU | P37551)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0045982    negative regulation of purine nucleobase metabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving purine nucleobases.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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  1p4a
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 Related Entries

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

UniProtKB/Swiss-Prot
        PURR_BACSU | P37551: 1o57

(-) Related Entries Specified in the PDB File

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