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(-) Description

Title :  CRYSTAL STRUCTURE OF SPX IN COMPLEX WITH THE C-TERMINAL DOMAIN OF THE RNA POLYMERASE ALPHA SUBUNIT
 
Authors :  K. J. Newberry, S. Nakano, P. Zuber, R. G. Brennan
Date :  11 Mar 05  (Deposition) - 11 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bacterial Transcription Regulation, Disulfide Stress (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Newberry, S. Nakano, P. Zuber, R. G. Brennan
Crystal Structure Of The Bacillus Subtilis Anti-Alpha, Global Transcriptional Regulator, Spx, In Complex With The {Alpha} C-Terminal Domain Of Rna Polymerase
Proc. Natl. Acad. Sci. Usa V. 102 15839 2005
PubMed-ID: 16249335  |  Reference-DOI: 10.1073/PNAS.0506592102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REGULATORY PROTEIN SPX
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PSN17
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: TRANSCRIPTION REGULATOR
    Gene: SPXA
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
 
Molecule 2 - DNA-DIRECTED RNA POLYMERASE ALPHA CHAIN
    Chains: B
    EC Number: 2.7.7.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PSN106
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN OF RNA POLYMERASE ALPHA SUBUNIT
    Gene: RPOA
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: RNAP ALPHA SUBUNIT, TRANSCRIPTASE ALPHA CHAIN, RNA POLYMERASE ALPHA SUBUNIT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:0 , MET A:1 , VAL A:63 , GLU A:85 , HIS A:86 , ASP A:97 , GLU A:98 , HOH A:409 , HOH A:410 , HOH A:449BINDING SITE FOR RESIDUE SO4 A 400
2AC2SOFTWARECYS A:10 , THR A:11 , SER A:12 , ARG A:92 , SO4 A:403BINDING SITE FOR RESIDUE SO4 A 401
3AC3SOFTWARESER A:58 , ARG A:91 , ARG A:92 , SO4 A:401 , HOH A:442 , HOH A:471 , HOH A:473BINDING SITE FOR RESIDUE SO4 A 403
4AC4SOFTWAREHOH B:131 , LYS B:245 , LEU B:249 , GLY B:292 , ARG B:293 , LYS B:294BINDING SITE FOR RESIDUE SO4 B 402

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:10 -A:13

(-) 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 1Z3E)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARSCPS51353 ArsC family profile.SPX_BACSU1-131  1A:1-118

(-) Exons   (0, 0)

(no "Exon" information available for 1Z3E)

(-) 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:119
 aligned with SPX_BACSU | O31602 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:119
                             1                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109         
            SPX_BACSU     - -MVTLYTSPSCTSCRKARAWLEEHEIPFVERNIFSEPLSIDEIKQILRMTEDGTDEIISTRSKVFQKLNVNVESMPLQDLYRLINEHPGLLRRPIIIDEKRLQVGYNEDEIRRFLPRKV 118
               SCOP domains -d1z3ea1 A:1-114 Regulatory protein Spx                                                                            ---- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----ArsC-1z3eA01 A:5-113                                                                                         ----- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh...eeeee......hhhhhhhhhhh...hhhhh....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...eee....eee....hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ARSC  PDB: A:1-118 UniProt: 1-131                                                                                      PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1z3e A   0 HMVTLYTSPSCTSCRKARAWLEEHEIPFVERNIFSEPLSIDEIKQILRMTEDGTDEIISTRSKVFQKLNVNVESMPLQDLYRLINEHPGLLRRPIIIDEKRLQVGYNEDEIRRFLPRKV 118
                                     9        19        29        39        49        59        69        79        89        99       109         


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 d1z3eb1 B:245-311 C-terminal domain of RNA polymerase alpha subunit SCOP domains
               CATH domains 1z3eB00 B:245-311 5' to 3' exonuclease, C-terminal subdomain        CATH domains
               Pfam domains RNA_pol_A_CTD-1z3eB01 B:245-305                              ------ Pfam domains
         Sec.struct. author hhhhhh.hhhhh..hhhhhhhhhhh...hhhhhhh.hhhhhhh....hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 1z3e B 245 KEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGLR 311
                                   254       264       274       284       294       304
   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  (2, 2)

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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Thioredoxin (367)
(-)
Clan: no clan defined [family: RNA_pol_A_CTD] (7)

(-) 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: 3gfk 3ihq
        SPX_BACSU | O31602: 3gfk 3ihq

(-) Related Entries Specified in the PDB File

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