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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES
 
Authors :  F. Lu, M. A. Schumacher, D. N. Arvidson, A. Haldimann, B. L. Wanner, H. Zalkin, R. G. Brennan
Date :  04 Oct 97  (Deposition) - 06 May 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Complex (Dna-Binding Protein/Dna), Dna-Binding Regulatory Protein, Extended Corepressor Specificity, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Lu, M. A. Schumacher, D. N. Arvidson, A. Haldimann, B. L. Wanner, H. Zalkin, R. G. Brennan
Structure-Based Redesign Of Corepressor Specificity Of The Escherichia Coli Purine Repressor By Substitution Of Residue 190.
Biochemistry V. 37 971 1998
PubMed-ID: 9454587  |  Reference-DOI: 10.1021/BI971942S
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*T )-3')
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 2 - PROTEIN (PURINE REPRESSOR)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPDNA100
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VectorPET24A
    GenePURR
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GUN1Ligand/IonGUANINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GUN2Ligand/IonGUANINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:71 , TYR A:73 , PHE A:74 , GLN A:190 , THR A:192 , ARG A:196 , PHE A:221 , ASP A:275 , HOH A:765BINDING SITE FOR RESIDUE GUN A 599

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PUF)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:265 -Pro A:266
2Thr A:284 -Pro A:285

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PUF)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LACI_1PS00356 LacI-type HTH domain signature.PURR_ECOLI4-22  1A:4-22
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LACI_1PS00356 LacI-type HTH domain signature.PURR_ECOLI4-22  2A:4-22

(-) Exons   (0, 0)

(no "Exon" information available for 2PUF)

(-) 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:338
 aligned with PURR_ECOLI | P0ACP7 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:338
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332        
           PURR_ECOLI     3 TIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDWGEAKADFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVADGPFRDYR 340
               SCOP domains d2pufa1 A:3-58                                          d2pufa2 A:59-340 Purine repressor (PurR), C-terminal domain                                                                                                                                                                                                                                SCOP domains
               CATH domains 2pufA01 A:3-59 lambda repressor-like DNA-binding domains 2pufA02 A:60-161,A:292-323  [code=3.40.50.2300, no name defined]                                      2pufA03 A:162-291,A:324-340  [code=3.40.50.2300, no name defined]                                                                 2pufA02 A:60-161,A:292-323      2pufA03           CATH domains
               Pfam domains LacI-2pufA01 A:3-48                           -------------------------------------------------------------------------------------------------------------------------Peripla_BP_3-2pufA02 A:170-331                                                                                                                                    --------- Pfam domains
         Sec.struct. author .hhhhhhh....hhhhhhhh.......hhhhhhhhhhhhh......hhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhh...eeee......hhhhhhhhhh....eee...........eeee..hhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhhh.....hhh.......hhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh...........................eee..hhhhhhhhhhhhhhhhh......eeee...eee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HTH_LACI_1         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2puf A   3 TIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDWGEAKADFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGPLEQNTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVADGPFRDYR 340
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332        

Chain B from PDB  Type:DNA  Length:17
                                                 
                 2puf B 699 TACGCAAACGTTTGCGT 715
                                   708       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (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 1jhz 1pnr 1pru 1prv 1qp0 1qp4 1qp7 1qpz 1qqa 1qqb 1vpw 1wet 1zay 2pua 2pub 2puc 2pud 2pue 2pug

(-) Related Entries Specified in the PDB File

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