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(-) Description

Title :  CRYSTAL STRUCTURE OF CBNR, A LYSR FAMILY TRANSCRIPTIONAL REGULATOR
 
Authors :  S. Muraoka, R. Okumura, N. Ogawa, K. Miyashita, T. Senda
Date :  18 Sep 02  (Deposition) - 06 May 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,P,Q
Keywords :  Long Alpha Helix Connecting Dna Binding And Regulatory Domains, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Muraoka, R. Okumura, N. Ogawa, T. Nonaka, K. Miyashita, T. Senda
Crystal Structure Of A Full-Length Lysr-Type Transcriptional Regulator, Cbnr: Unusual Combination Of Two Subunit Forms And Molecular Bases For Causing And Changing Dna Bend
J. Mol. Biol. V. 328 555 2003
PubMed-ID: 12706716  |  Reference-DOI: 10.1016/S0022-2836(03)00312-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LYSR-TYPE REGULATORY PROTEIN
    Chains: A, B, P, Q
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: CUPRIAVIDUS NECATOR
    Organism Taxid: 106590
    Synonym: CBNR

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABPQ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1IZ1)

(-) Sites  (0, 0)

(no "Site" information available for 1IZ1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IZ1)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Phe A:194 -Pro A:195
2Arg A:199 -Pro A:200
3Phe B:194 -Pro B:195
4Arg B:199 -Pro B:200
5Phe P:194 -Pro P:195
6Arg P:199 -Pro P:200
7Phe Q:194 -Pro Q:195
8Arg Q:199 -Pro Q:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IZ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IZ1)

(-) Exons   (0, 0)

(no "Exon" information available for 1IZ1)

(-) 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:292
 aligned with Q9WXC7_CUPNE | Q9WXC7 from UniProtKB/TrEMBL  Length:294

    Alignment length:292
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290  
         Q9WXC7_CUPNE     1 MEFRQLKYFIAVAEAGNMAAAAKRLHVSQPPITRQMQALEADLGVVLLERSHRGIELTAAGHAFLEDARRILELAGRSGDRSRAAARGDVGELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIEIVNIAQEDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAGAASSIVPASVAAIRWPDIAFARIVGTRVKVPISCIFRKEKQPPILARFVEHVRRSA 292
               SCOP domains d1iz1a1 A:1-89 LysR-type regulatory protein CbnR                                         d1iz1a2 A:90-292 LysR-type regulatory protein CbnR                                                                                                                                                          SCOP domains
               CATH domains -1iz1A01 A:2-87 'winged helix' repressor DNA binding domain                            1iz1A02 A:88-161,A:268-292 Periplasmic binding protein-like II            1iz1A03 A:162-267 Periplasmic binding protein-like II                                                     1iz1A02                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeee.hhhhhh..eehhhhhh...eee.......hhhhhhhhhhhhh.....eeee..hhhhhhhhhhh...eeeeehhhhh.....eeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iz1 A   1 MEFRQLKYFIAVAEAGNMAAAAKRLHVSQPPITRQMQALEADLGVVLLERSHRGIELTAAGHAFLEDARRILELAGRSGDRSRAAARGDVGELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIEIVNIAQEDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAGAASSIVPASVAAIRWPDIAFARIVGTRVKVPISCIFRKEKQPPILARFVEHVRRSA 292
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290  


Chain B from PDB  Type:PROTEIN  Length:294
 aligned with Q9WXC7_CUPNE | Q9WXC7 from UniProtKB/TrEMBL  Length:294

    Alignment length:294
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290    
         Q9WXC7_CUPNE     1 MEFRQLKYFIAVAEAGNMAAAAKRLHVSQPPITRQMQALEADLGVVLLERSHRGIELTAAGHAFLEDARRILELAGRSGDRSRAAARGDVGELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIEIVNIAQEDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAGAASSIVPASVAAIRWPDIAFARIVGTRVKVPISCIFRKEKQPPILARFVEHVRRSAKD 294
               SCOP domains d1iz1b1 B:1-89 LysR-type regulatory protein CbnR                                         d1iz1b2 B:90-294 LysR-type regulatory protein CbnR                                                                                                                                                            SCOP domains
               CATH domains ------1iz1B01 B:7-87 'winged helix' repressor DNA binding domain                       1iz1B02 B:88-161,B:268-293 Periplasmic binding protein-like II            1iz1B03 B:162-267 Periplasmic binding protein-like II                                                     1iz1B02 B:88-161,B:268-293- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...eee....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeee.hhhhhh..eehhhhhh..eeee.......hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh...eeeeehhhhhh....eeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1iz1 B   1 MEFRQLKYFIAVAEAGNMAAAAKRLHVSQPPITRQMQALEADLGVVLLERSHRGIELTAAGHAFLEDARRILELAGRSGDRSRAAARGDVGELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIEIVNIAQEDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAGAASSIVPASVAAIRWPDIAFARIVGTRVKVPISCIFRKEKQPPILARFVEHVRRSAKD 294
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290    


Chain P from PDB  Type:PROTEIN  Length:292
 aligned with Q9WXC7_CUPNE | Q9WXC7 from UniProtKB/TrEMBL  Length:294

    Alignment length:292
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290  
         Q9WXC7_CUPNE     1 MEFRQLKYFIAVAEAGNMAAAAKRLHVSQPPITRQMQALEADLGVVLLERSHRGIELTAAGHAFLEDARRILELAGRSGDRSRAAARGDVGELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIEIVNIAQEDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAGAASSIVPASVAAIRWPDIAFARIVGTRVKVPISCIFRKEKQPPILARFVEHVRRSA 292
               SCOP domains d1iz1p1 P:1-89 LysR-type regulatory protein CbnR                                         d1iz1p2 P:90-292 LysR-type regulatory protein CbnR                                                                                                                                                          SCOP domains
               CATH domains -1iz1P01 P:2-87 'winged helix' repressor DNA binding domain                            1iz1P02 P:88-161,P:268-292 Periplasmic binding protein-like II            1iz1P03 P:162-267 Periplasmic binding protein-like II                                                     1iz1P02                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...ee......eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh...eeee........eeeeeeeeeeeeeeee..hhhhhh.eehhhhhh...eee.......hhhhhhhhhhhhh.....eeee..hhhhhhhhhhh....eeeehhhhh.....eeeeee.....eeeeeeeee....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iz1 P   1 MEFRQLKYFIAVAEAGNMAAAAKRLHVSQPPITRQMQALEADLGVVLLERSHRGIELTAAGHAFLEDARRILELAGRSGDRSRAAARGDVGELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIEIVNIAQEDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAGAASSIVPASVAAIRWPDIAFARIVGTRVKVPISCIFRKEKQPPILARFVEHVRRSA 292
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290  


Chain Q from PDB  Type:PROTEIN  Length:292
 aligned with Q9WXC7_CUPNE | Q9WXC7 from UniProtKB/TrEMBL  Length:294

    Alignment length:292
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290  
         Q9WXC7_CUPNE     1 MEFRQLKYFIAVAEAGNMAAAAKRLHVSQPPITRQMQALEADLGVVLLERSHRGIELTAAGHAFLEDARRILELAGRSGDRSRAAARGDVGELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIEIVNIAQEDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAGAASSIVPASVAAIRWPDIAFARIVGTRVKVPISCIFRKEKQPPILARFVEHVRRSA 292
               SCOP domains d1iz1q1 Q:1-89 LysR-type regulatory protein CbnR                                         d1iz1q2 Q:90-292 LysR-type regulatory protein CbnR                                                                                                                                                          SCOP domains
               CATH domains ------1iz1Q01 Q:7-87 'winged helix' repressor DNA binding domain                       1iz1Q02 Q:88-161,Q:268-292 Periplasmic binding protein-like II            1iz1Q03 Q:162-267 Periplasmic binding protein-like II                                                     1iz1Q02                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...ee......eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh.....eee........eeeeeeeee.eeeeee.hhhhhh..eehhhhhh..eeee.......hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh...eeeeehhhhh.....eeeeee......eeeeeeee....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iz1 Q   1 MEFRQLKYFIAVAEAGNMAAAAKRLHVSQPPITRQMQALEADLGVVLLERSHRGIELTAAGHAFLEDARRILELAGRSGDRSRAAARGDVGELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIEIVNIAQEDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAGAASSIVPASVAAIRWPDIAFARIVGTRVKVPISCIFRKEKQPPILARFVEHVRRSA 292
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   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  (2, 8)

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

(-) CATH Domains  (2, 12)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Architecture: 3-Layer(aba) Sandwich (12045)
(-)
Topology: D-Maltodextrin-Binding Protein; domain 2 (600)
(-)
Homologous Superfamily: Periplasmic binding protein-like II (486)
(-)
Cupriavidus necator. Organism_taxid: 106590. (1)
1a1iz1A03A:162-267
1b1iz1B03B:162-267
1c1iz1P03P:162-267
1d1iz1Q03Q:162-267
1e1iz1B02B:88-161,B:268-293
1f1iz1A02A:88-161,A:268-292
1g1iz1P02P:88-161,P:268-292
1h1iz1Q02Q:88-161,Q:268-292
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IZ1)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,P,Q   (Q9WXC7_CUPNE | Q9WXC7)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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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  Cis Peptide Bonds
    Arg A:199 - Pro A:200   [ RasMol ]  
    Arg B:199 - Pro B:200   [ RasMol ]  
    Arg P:199 - Pro P:200   [ RasMol ]  
    Arg Q:199 - Pro Q:200   [ RasMol ]  
    Phe A:194 - Pro A:195   [ RasMol ]  
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    Phe P:194 - Pro P:195   [ RasMol ]  
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 Related Entries

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

UniProtKB/TrEMBL
        Q9WXC7_CUPNE | Q9WXC7: 1ixc

(-) Related Entries Specified in the PDB File

1ixc 1IXC CONTAINS CRYSTAL STRUCTURE OF THE SAME PROTEIN WITH SELENOMETHIONINE