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(-) Description

Title :  THE STRUCTURE OF A REDUCED FORM OF OXYR FROM N. MENINGITIDIS
 
Authors :  S. Sainsbury, J. Ren, D. I. Stuart, R. J. Owens, Oxford Protein Produc Facility (Oppf)
Date :  16 Sep 09  (Deposition) - 16 Jun 10  (Release) - 16 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lysr-Type Transcriptional Regulator, Lttr, Redox, Structural Genomics, Oppf, Oxford Protein Production Facility, Dna-Binding, Transcription, Transcription Regulation, Oppf3291 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Sainsbury, J. Ren, J. E. Nettleship, N. J. Saunders, D. I. Stuart, R. J. Owens
The Structure Of A Reduced Form Of Oxyr From Neisseria Meningitidis
Bmc Struct. Biol. V. 10 10 2010
PubMed-ID: 20478059  |  Reference-DOI: 10.1186/1472-6807-10-10

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR, LYSR FAMILY
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: OPPF3291
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 88-306
    Gene: NMB0173
    Organism Scientific: NEISSERIA MENINGITIDIS
    Organism Taxid: 122586
    Strain: MC58
    Synonym: OXYR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric/Biological Unit (2, 18)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:129 , HIS A:130 , GLY A:197BINDING SITE FOR RESIDUE CL A 307
2AC2SOFTWARESER B:228 , ILE B:229BINDING SITE FOR RESIDUE CL B 78

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JV9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:148 -Pro A:149
2Glu B:148 -Pro B:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JV9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JV9)

(-) Exons   (0, 0)

(no "Exon" information available for 3JV9)

(-) 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:216
 aligned with Q9K1H8_NEIMB | Q9K1H8 from UniProtKB/TrEMBL  Length:306

    Alignment length:216
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299      
         Q9K1H8_NEIMB    90 EGAFKLGLIFTVAPYLLPKLIVSLRRTAPKMPLMLEENYTHTLTESLKRGDVDAIIVAEPFQEPGIVTEPLYDEPFFVIVPKGHSFEELDAVSPRMLGEEQVLLLTEGNCMRDQVLSSCSELAAKQRIQGLTNTLQGSSINTIRHMVASGLAISVLPATALTENDHMLFSIIPFEGTPPSRRVVLAYRRNFVRPKALSAMKAAIMQSQLHGVSFIC 305
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh....eeeee.......eeeeeeeeeeeeeeee..hhhhh.............eeee...hhhhhhhhhhh..hhhhhhhhh.....ee.hhhhhhhhhhhh..eeeee.hhh.......eeee.......eeeeeeeee....hhhhhhhhhhhhhh......ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3jv9 A  90 EGAFKLGLIFTVAPYLLPKLIVSLRRTAPKmPLmLEENYTHTLTESLKRGDVDAIIVAEPFQEPGIVTEPLYDEPFFVIVPKGHSFEELDAVSPRmLGEEQVLLLTEGNCmRDQVLSSCSELAAKQRIQGLTNTLQGSSINTIRHmVASGLAISVLPATALTENDHmLFSIIPFEGTPPSRRVVLAYRRNFVRPKALSAmKAAImQSQLHGVSFIC 305
                                    99       109       119|  |   129       139       149       159       169       179     | 189       199|      209       219       229     | 239       249      |259       269       279       289    |  299      
                                                        120-MSE                                                          185-MSE        200-MSE                            235-MSE              256-MSE                          289-MSE|           
                                                           123-MSE                                                                                                                                                                    294-MSE       


Chain B from PDB  Type:PROTEIN  Length:204
 aligned with Q9K1H8_NEIMB | Q9K1H8 from UniProtKB/TrEMBL  Length:306

    Alignment length:216
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299      
         Q9K1H8_NEIMB    90 EGAFKLGLIFTVAPYLLPKLIVSLRRTAPKMPLMLEENYTHTLTESLKRGDVDAIIVAEPFQEPGIVTEPLYDEPFFVIVPKGHSFEELDAVSPRMLGEEQVLLLTEGNCMRDQVLSSCSELAAKQRIQGLTNTLQGSSINTIRHMVASGLAISVLPATALTENDHMLFSIIPFEGTPPSRRVVLAYRRNFVRPKALSAMKAAIMQSQLHGVSFIC 305
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) LysR_substrate-3jv9B01 B:90-297                                                                                                                                                                                 -------- Pfam domains (1)
           Pfam domains (2) LysR_substrate-3jv9B02 B:90-297                                                                                                                                                                                 -------- Pfam domains (2)
         Sec.struct. author ...eeeeee..hhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh....eeeee.......eeeeeeeeeeeeeeee..hhhhhh.....hhhhhh.eeee...hhhhhhhhh..------------....ee.hhhhhhhhhhh...eeeee.hhhhhhhhh.eeeee......eeeeeeeee....hhhhhhhhhhhhhh......ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3jv9 B  90 EGAFKLGLIFTVAPYLLPKLIVSLRRTAPKmPLmLEENYTHTLTESLKRGDVDAIIVAEPFQEPGIVTEPLYDEPFFVIVPKGHSFEELDAVSPRmLGEEQVLLLTEGNCmRDQVLSSC------------TNTLQGSSINTIRHmVASGLAISVLPATALTENDHmLFSIIPFEGTPPSRRVVLAYRRNFVRPKALSAmKAAImQSQLHGVSFIC 305
                                    99       109       119|  |   129       139       149       159       169       179     | 189       199|       |-         - |     229     | 239       249      |259       269       279       289    |  299      
                                                        120-MSE                                                          185-MSE        200-MSE 208          221           235-MSE              256-MSE                          289-MSE|           
                                                           123-MSE                                                                                                                                                                    294-MSE
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 3JV9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JV9)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9K1H8_NEIMB | Q9K1H8)
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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 Related Entries

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