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(-) Description

Title :  SOLUTION NMR REFINEMENT OF A METAL ION BOUND PROTEIN USING QUANTUM MECHANICAL/MOLECULAR MECHANICAL AND MOLECULAR DYNAMICS METHODS
 
Authors :  D. K. Chakravorty, B. I. Wang, C. I. Lee, A. J. Guerra, D. P. Giedroc, K. M. A. I. Arunkumar, M. Pennella, X. Kong
Date :  04 Jan 13  (Deposition) - 08 May 13  (Release) - 24 Jul 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (10x)
NMR Structure *:  A,B  (1x)
Keywords :  Metal Ion Refinement, Transcription Repressor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. K. Chakravorty, B. Wang, C. W. Lee, A. J. Guerra, D. P. Giedroc, K. M. Merz
Solution Nmr Refinement Of A Metal Ion Bound Protein Using Metal Ion Inclusive Restrained Molecular Dynamics Methods.
J. Biomol. Nmr V. 56 125 2013
PubMed-ID: 23609042  |  Reference-DOI: 10.1007/S10858-013-9729-7

(-) Compounds

Molecule 1 - REPRESSOR PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET3A
    Gene: CZRA
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 Structural Features

(-) Chains, Units

  12
NMR Structure (10x): AB
NMR Structure * (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
NMR Structure * (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:97 , HIS A:100 , ASP B:84 , HIS B:86BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREASP A:84 , HIS A:86 , HIS B:97 , HIS B:100BINDING SITE FOR RESIDUE ZN B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2M30)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2M30)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2M30)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2M30)

(-) Exons   (0, 0)

(no "Exon" information available for 2M30)

(-) Sequences/Alignments

NMR Structure
   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:95
 aligned with O85142_STAAU | O85142 from UniProtKB/TrEMBL  Length:106

    Alignment length:95
                                    18        28        38        48        58        68        78        88        98     
         O85142_STAAU     9 NTDTLERVTEIFKALGDYNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQSMIYSLDDIHVATMLKQAIHHANHPKE 103
               SCOP domains d2m30a_ A: Metal-sensing transcriptional repressor CzrA                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh....hhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..eeeeee.hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 2m30 A   9 NTDTLERVTEIFKALGDYNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQSMIYSLDDIHVATMLKQAIHHANHPKE 103
                                    18        28        38        48        58        68        78        88        98     


Chain B from PDB  Type:PROTEIN  Length:95
 aligned with O85142_STAAU | O85142 from UniProtKB/TrEMBL  Length:106

    Alignment length:95
                                    18        28        38        48        58        68        78        88        98     
         O85142_STAAU     9 NTDTLERVTEIFKALGDYNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQSMIYSLDDIHVATMLKQAIHHANHPKE 103
               SCOP domains d2m30b_ B: Metal-sensing transcriptional repressor CzrA                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..eeeeee.hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 2m30 B   9 NTDTLERVTEIFKALGDYNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQSMIYSLDDIHVATMLKQAIHHANHPKE 103
                                    18        28        38        48        58        68        78        88        98
   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  (1, 2)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2M30)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2M30)

(-) Gene Ontology  (5, 5)

NMR Structure(hide GO term definitions)
Chain A,B   (O85142_STAAU | O85142)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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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  2m30
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  O85142_STAAU | O85142
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 Related Entries

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

UniProtKB/TrEMBL
        O85142_STAAU | O85142: 1r1u 1r1v 2kjb 2kjc

(-) Related Entries Specified in the PDB File

7376
1r1u CRYSTAL STRUCTURE OF THE APO-FORM OF THIS REPRESSOR
1r1v CRYSTAL STRUCTURE OF ZN-BOUND FORM OF THIS REPRESSOR
2kjb SOLUTION STRUCTURE OF THIS REPRESSOR IN THE DNA BOUND STATE
2kjc SOLUTION STRUCTURE OF THIS REPRESSOR IN THE ZN-BOUND STATE