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(-) Description

Title :  PURINE REPRESSOR MUTANT COREPRESSOR BINDING DOMAIN STRUCTURE
 
Authors :  J. L. Huffman, F. Lu, H. Zalkin, R. G. Brennan
Date :  28 Jun 01  (Deposition) - 08 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Corepressor Binding Domain, Purine Repressor, Allosteric Regulation, Dna-Binding Protein, Purine Biosynthesis, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. L. Huffman, F. Lu, H. Zalkin, R. G. Brennan
Role Of Residue 147 In The Gene Regulatory Function Of The Escherichia Coli Purine Repressor.
Biochemistry V. 41 511 2002
PubMed-ID: 11781089  |  Reference-DOI: 10.1021/BI0156660
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PURINE NUCLEOTIDE SYNTHESIS REPRESSOR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24A
    Expression System StrainBL21 LAMBDA DE3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCOREPRESSOR-FREE COREPRESSOR BINDING DOMAIN (RESIDUES 53-341)
    GenePURR
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:490 , GLU B:70BINDING SITE FOR RESIDUE MG B 401
2AC2SOFTWAREGLU A:320 , HOH A:464BINDING SITE FOR RESIDUE MG A 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Val A:265 -Pro A:266
2Thr A:284 -Pro A:285
3Val B:265 -Pro B:266
4Thr B:284 -Pro B:285

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1JHZ)

(-) 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:276
 aligned with PURR_ECOLI | P0ACP7 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:282
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  
           PURR_ECOLI    60 KSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDWGEAKADFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVADGPFRDYRR 341
               SCOP domains d1jhza_ A: Purine repressor (PurR), C-terminal domain                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1jhzA01 A:60-161,A:292-323  [code=3.40.50.2300, no name defined]                                      1jhzA02 A:162-291,A:324-34      0  [code=3.40.50.2300, no name defined]                                                           1jhzA01 A:60-161,A:292-323      1jhzA02          - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh....eeeee.........eeee.hhhhhhhhhhhhhhhh....eeee...------hhhhhhhhhhhhhh....hhhh......hhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhh........eee....hhhhhhh.....eee.hhhhhhhhhhhhhhhhhh.......eee...eee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jhz A  60 KSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDFGEAKADFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGP------AGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVADGPFRDYRR 341
                                    69        79        89        99       109       119       129       139       149       159       169       179       | -    |  199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  
                                                                                                                                                         187    194                                                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:276
 aligned with PURR_ECOLI | P0ACP7 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:282
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  
           PURR_ECOLI    60 KSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDWGEAKADFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVADGPFRDYRR 341
               SCOP domains d1jhzb_ B: Purine repressor (PurR), C-terminal domain                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1jhzB01 B:60-161,B:292-323  [code=3.40.50.2300, no name defined]                                      1jhzB02 B:162-291,B:324-34      0  [code=3.40.50.2300, no name defined]                                                           1jhzB01 B:60-161,B:292-323      1jhzB02          - CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------Peripla_BP_3-1jhzB      01 B:170-331                                                                                                                              ---------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------Peripla_BP_3-1jhzB      02 B:170-331                                                                                                                              ---------- Pfam domains (2)
         Sec.struct. author .eeeeee.......hhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh......ee....hhhhhhhhhhh......eeee.........eee.hhhhhhhhhhhhhhhh....eeee...------hhhhhhhhhhhhhh....hhhh......hhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhh........eeeeee.hhhhhhh....eeee....hhhhhhhhhhhhhhh........ee...eee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jhz B  60 KSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDFGEAKADFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGP------AGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVADGPFRDYRR 341
                                    69        79        89        99       109       119       129       139       149       159       169       179       | -    |  199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  
                                                                                                                                                         187    194                                                                                                                                                   

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
1a1jhzA02A:162-291,A:324-340
1b1jhzB02B:162-291,B:324-340
1c1jhzA01A:60-161,A:292-323
1d1jhzB01B:60-161,B:292-323

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PURR_ECOLI | P0ACP7)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    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:0006164    purine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PURR_ECOLI | P0ACP71bdh 1bdi 1dbq 1jfs 1jft 1jh9 1pnr 1pru 1prv 1qp0 1qp4 1qp7 1qpz 1qqa 1qqb 1vpw 1wet 1zay 2pua 2pub 2puc 2pud 2pue 2puf 2pug

(-) Related Entries Specified in the PDB File

1jfs PURINE REPRESSOR MUTANT-HYPOXANTHINE-PURF OPERATOR COMPLEX (W147F)
1jft PURINE REPRESSOR MUTANT-HYPOXANTHINE-PURF OPERATOR COMPLEX (W147A)
1jh9 PURINE REPRESSOR MUTANT-HYPOXANTHINE-PURF OPERATOR COMPLEX (W147R)
1pnr PURINE REPRESSOR-HYPOXANTHINE-PURF-OPERATOR COMPLEX
1qpz PURINE REPRESSOR-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX