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(-) Description

Title :  CRYSTAL STRUCTURE OF REDUCED C10S SPX IN COMPLEX WITH THE ALPHA C-TERMINAL DOMAIN OF RNA POLYMERAS
 
Authors :  K. J. Newberry, R. G. Brennan
Date :  30 Jul 09  (Deposition) - 02 Feb 10  (Release) - 02 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription Regulation, Oxidative Stress, Spx, Rna Polymerase, Cytoplasm, Disulfide Bond, Redox-Active Center, Stress Response, Transcription, Dna-Directed Rna Polymerase, Nucleotidyltransferase, Transferase, Transcription/Transferase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Nakano, A. Lin, C. S. Zuber, K. J. Newberry, R. G. Brennan, P. Zuber
Promoter Recognition By A Complex Of Spx And The C-Terminal Domain Of The Rna Polymerase Alpha Subunit.
Plos One V. 5 E8664 2010
PubMed-ID: 20084284  |  Reference-DOI: 10.1371/JOURNAL.PONE.0008664
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REGULATORY PROTEIN SPX
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEX
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BSU11500, SPXA
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
 
Molecule 2 - DNA-DIRECTED RNA POLYMERASE SUBUNIT ALPHA
    Chains: B
    EC Number: 2.7.7.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ROSETTA 2 (BL21)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 245-314
    Gene: BSU01430, RPOA
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: RNAP SUBUNIT ALPHA, TRANSCRIPTASE SUBUNIT ALPHA, RNA POLYMERASE SUBUNIT ALPHA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1IMD1Ligand/IonIMIDAZOLE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:59 , ARG A:60 , ARG A:91BINDING SITE FOR RESIDUE IMD A 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:92 -Pro A:93

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARSCPS51353 ArsC family profile.SPX_BACSU1-131  1A:1-115

(-) Exons   (0, 0)

(no "Exon" information available for 3IHQ)

(-) 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:115
 aligned with SPX_BACSU | O31602 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:115
                                    10        20        30        40        50        60        70        80        90       100       110     
            SPX_BACSU     1 MVTLYTSPSCTSCRKARAWLEEHEIPFVERNIFSEPLSIDEIKQILRMTEDGTDEIISTRSKVFQKLNVNVESMPLQDLYRLINEHPGLLRRPIIIDEKRLQVGYNEDEIRRFLP 115
               SCOP domains d3ihqa_ A: automated matches                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh...eeeee......hhhhhhhhhhh...hhhhh..................hhhhhhhhhhhhhhhh...eee....eee....hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ARSC  PDB: A:1-115 UniProt: 1-131                                                                                   PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3ihq A   1 MVTLYTSPSSTSCRKARAWLEEHEIPFVERNIFSEPLSIDEIKQILRMTEDGTDEIISTRSKVFQKLNVNVESMPLQDLYRLINEHPGLLRRPIIIDEKRLQVGYNEDEIRRFLP 115
                                    10        20        30        40        50        60        70        80        90       100       110     


Chain B from PDB  Type:PROTEIN  Length:67
 aligned with RPOA_BACSU | P20429 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:67
                                   254       264       274       284       294       304       
           RPOA_BACSU   245 KEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGLR 311
               SCOP domains d3ihqb_ B: automated matches                                        SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.hhhhh..hhhhhhhhhhh...hhhhhhh.hhhhhhh....hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 3ihq B 245 KEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGLR 311
                                   254       264       274       284       294       304
   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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SPX_BACSU | O31602)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B   (RPOA_BACSU | P20429)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003899    DNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RPOA_BACSU | P20429: 1z3e 3gfk
        SPX_BACSU | O31602: 1z3e 3gfk

(-) Related Entries Specified in the PDB File

1z3e OXIDIZED SPX STRUCTURE