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(-) Description

Title :  CRYSTAL STRUCTURE OF A NITROGEN REPRESSOR-LIKE PROTEIN MJ0159 FROM METHANOCOCCUS JANNASCHII
 
Authors :  J. B. Bonanno, Y. Patskovsky, V. Malashkevich, S. Ozyurt, M. Dickey, B. M. Maletic, L. Rodgers, J. Koss, J. M. Sauder, S. K. Burley, S. C. Almo, N Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  09 Jun 10  (Deposition) - 23 Jun 10  (Release) - 05 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Unknown Function, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Wisedchaisri, D. M. Dranow, T. J. Lie, J. B. Bonanno, Y. Patskovsky, S. A. Ozyurt, J. M. Sauder, S. C. Almo, S. R. Wasserman, S. K. Burley, J. A. Leigh, T. Gonen
Structural Underpinnings Of Nitrogen Regulation By The Prototypical Nitrogen-Responsive Transcriptional Factor Nrpr.
Structure V. 18 1512 2010
PubMed-ID: 21070950  |  Reference-DOI: 10.1016/J.STR.2010.08.014

(-) Compounds

Molecule 1 - NITROGEN REPRESSOR-LIKE PROTEIN MJ0159
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET26
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MJ0159
    Organism Common: METHANOCOCCUS JANNASCHII
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric/Biological Unit (2, 13)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:350 , ALA A:396 , TYR A:433 , HIS A:441 , ARG A:459 , GLY A:508BINDING SITE FOR RESIDUE GOL A 1
2AC2SOFTWARELYS A:482 , MSE A:506 , TYR A:539BINDING SITE FOR RESIDUE GOL A 3
3AC3SOFTWAREASN B:350 , ALA B:396 , TYR B:433 , HIS B:441 , GLY B:508 , ILE B:509BINDING SITE FOR RESIDUE GOL B 2

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NEK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NEK)

(-) 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:220
 aligned with NRPR_METJA | Q57623 from UniProtKB/Swiss-Prot  Length:542

    Alignment length:220
                                   330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540
           NRPR_METJA   321 RIKTALSKMFNAMAKVTYDIDEADGDVIVNTAFIDKKYLDEAFDILKEAYKKGLGISDRFGIVEENDRIKIQTICAVTLDGIFLRNSVPLIPKYGGILEITEDKERFIDIIGYDGSSLDPHEVFFNFVDCEKTFLAGFREVHRVAREKLEEVLKKLNWNGIKAIGEPNNELYGIGVNKDMCGVVTMGGINPLVLLKENEIPIELKAMHEVVRFSDLKSYK 540
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...........eeeeeeeeee..hhhhhhhhhhhhhhh......eeeeee...eeeeeee.hhhhhhhhhhh...eeeeeeeeeee....eeeeeeee......hhhhhhhhhh....eeeeeeeeee..hhhhhhhhhhhhh...eeee...............eeeeeee..hhhhhhhhhh....eeeeeeeeee.hhhee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nek A 321 RIKTALSKmFNAmAKVTYDIDEADGDVIVNTAFIDKKYLDEAFDILKEAYKKGLGISDRFGIVEENDRIKIQTICAVTLDGIFLRNSVPLIPKYGGILEITEDKERFIDIIGYDGSSLDPHEVFFNFVDCEKTFLAGFREVHRVAREKLEEVLKKLNWNGIKAIGEPNNELYGIGVNKDmCGVVTmGGINPLVLLKENEIPIELKAmHEVVRFSDLKSYK 540
                                   330  |    340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500     | 510       520      |530       540
                                  329-MSE                                                                                                                                                                    500-MSE |                  527-MSE         
                                      333-MSE                                                                                                                                                                      506-MSE                              


Chain B from PDB  Type:PROTEIN  Length:221
 aligned with NRPR_METJA | Q57623 from UniProtKB/Swiss-Prot  Length:542

    Alignment length:221
                                   328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538 
           NRPR_METJA   319 NIRIKTALSKMFNAMAKVTYDIDEADGDVIVNTAFIDKKYLDEAFDILKEAYKKGLGISDRFGIVEENDRIKIQTICAVTLDGIFLRNSVPLIPKYGGILEITEDKERFIDIIGYDGSSLDPHEVFFNFVDCEKTFLAGFREVHRVAREKLEEVLKKLNWNGIKAIGEPNNELYGIGVNKDMCGVVTMGGINPLVLLKENEIPIELKAMHEVVRFSDLKSY 539
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh.........eeeeeeeeee..hhhhhhhhhhhhhhh......eeeeee...eeeeeeehhhhhhhhhhh....eeeeeeeeeee....eeeeeeee......hhhhhhhhhh....eeeeeeeeee..hhhhhhhhhhhhh...eeee...............eeeeeee..hhhhhhhhhh....eeeeeeeeee.hhhee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nek B 319 NIRIKTALSKmFNAmAKVTYDIDEADGDVIVNTAFIDKKYLDEAFDILKEAYKKGLGISDRFGIVEENDRIKIQTICAVTLDGIFLRNSVPLIPKYGGILEITEDKERFIDIIGYDGSSLDPHEVFFNFVDCEKTFLAGFREVHRVAREKLEEVLKKLNWNGIKAIGEPNNELYGIGVNKDmCGVVTmGGINPLVLLKENEIPIELKAmHEVVRFSDLKSY 539
                                   328|   |  338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498 |     508       518       528       538 
                                    329-MSE                                                                                                                                                                    500-MSE |                  527-MSE        
                                        333-MSE                                                                                                                                                                      506-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  (0, 0)

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

(-) CATH Domains  (0, 0 ; only for superseded entry 2QYX: 1,4)

(no "CATH Domain" information available for 3NEK, only for superseded entry 2QYX replaced by 3NEK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3NEK)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NRPR_METJA | Q57623)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
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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