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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 Jun 02  (Deposition) - 18 Jun 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
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 Transcriptiona 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

(-) Compounds

Molecule 1 - LYSR-TYPE REGULATORY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7-7
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CBNR
    Organism Scientific: CUPRIAVIDUS NECATOR
    Organism Taxid: 106590
    Synonym: CBNR

 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, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 20)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1IXC)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Phe A:194 -Pro A:195
2Arg A:199 -Pro A:200
3Phe B:194 -Pro B:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1IXC)

(-) 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:289
 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 d1ixca1 A:1-89 LysR-type regulatory protein CbnR                                         d1ixca2 A:90-294 LysR-type regulatory protein CbnR                                                                                                                                                            SCOP domains
               CATH domains -1ixcA01 A:2-87 'winged helix' repressor DNA bind     ing domain                       1ixcA02 A:88-161,A:268-293 Periplasmic binding protein-like II            1ixcA03 A:162-267 Periplasmic binding protein-like II                                                     1ixcA02 A:88-161,A:268-293- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.....-----...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeee.hhhhhh..eehhhhhh...eee.......hhhhhhhhhhhhh.....eeee..hhhhhhhhhhh...eeeeehhhhh.....eeeeee.....eeeeeeeee....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ixc A   1 mEFRQLKYFIAVAEAGNmAAAAKRLHVSQPPITRQmQALEADLGVVLLE-----IELTAAGHAFLEDARRILELAGRSGDRSRAAARGDVGELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHmTKDEQVEGLLAGTIHVGFSRFFPRHPGIEIVNIAQEDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTmAGAASSIVPASVAAIRWPDIAFARIVGTRVKVPISCIFRKEKQPPILARFVEHVRRSAKD 294
                            |       10       |20        30     |  40        |-    |   60        70        80        90       100       110       120      |130       140       150       160       170       180       190       200       210       220       230   |   240       250       260       270       280       290    
                            |               18-MSE            36-MSE       49    55                                                                     127-MSE                                                                                                    234-MSE                                                        
                            1-MSE                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:289
 aligned with Q9WXC7_CUPNE | Q9WXC7 from UniProtKB/TrEMBL  Length:294

    Alignment length:289
                                    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         
         Q9WXC7_CUPNE     1 MEFRQLKYFIAVAEAGNMAAAAKRLHVSQPPITRQMQALEADLGVVLLERSHRGIELTAAGHAFLEDARRILELAGRSGDRSRAAARGDVGELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIEIVNIAQEDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAGAASSIVPASVAAIRWPDIAFARIVGTRVKVPISCIFRKEKQPPILARFVEHVR 289
               SCOP domains d1ixcb1 B:1-89 LysR-type regulatory protein CbnR                                         d1ixcb2 B:90-289 LysR-type regulatory protein CbnR                                                                                                                                                       SCOP domains
               CATH domains ------1ixcB01 B:7-87 'winged helix' repressor DNA binding domain                       1ixcB02 B:88-161,B:268-289 Periplasmic binding protein-like II            1ixcB03 B:162-267 Periplasmic binding protein-like II                                                     1ixcB02                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeee.hhh.....eehhhhhh..eeee.......hhhhhhhhhhhhh....eeeee..hhhhhhhhhhh...eeeeehhhhh.....eeeeee.....eeeeeeeee....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ixc B   1 mEFRQLKYFIAVAEAGNmAAAAKRLHVSQPPITRQmQALEADLGVVLLERSHRGIELTAAGHAFLEDARRILELAGRSGDRSRAAARGDVGELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHmTKDEQVEGLLAGTIHVGFSRFFPRHPGIEIVNIAQEDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTmAGAASSIVPASVAAIRWPDIAFARIVGTRVKVPISCIFRKEKQPPILARFVEHVR 289
                            |       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         
                            1-MSE           18-MSE            36-MSE                                                                                    127-MSE                                                                                                    234-MSE
   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, 4)

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

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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
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 Related Entries

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        Q9WXC7_CUPNE | Q9WXC7: 1iz1

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