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(-) Description

Title :  STRUCTURAL BASIS OF THE NUCLEOTIDE DRIVEN CONFORMATIONAL CHANGES IN THE AAA DOMAIN OF TRANSCRIPTION ACTIVATOR PSPF
 
Authors :  M. Rappas, J. Schumacher, H. Niwa, M. Buck, X. Zhang
Date :  09 Dec 05  (Deposition) - 01 Feb 06  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Bacterial Sigma54 Activator, Atpase, Atp-Binding, Dna-Binding, Sensory Transduction, Transcription Regulation, Two-Component Regulatory System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Rappas, J. Schumacher, H. Niwa, M. Buck, X. Zhang
Structural Basis Of The Nucleotide Driven Conformational Changes In The Aaa(+) Domain Of Transcription Activator Pspf.
J. Mol. Biol. V. 357 481 2006
PubMed-ID: 16430918  |  Reference-DOI: 10.1016/J.JMB.2005.12.052

(-) Compounds

Molecule 1 - PSP OPERON TRANSCRIPTIONAL ACTIVATOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector: PET28B
    Fragment: AAA DOMAIN, RESIDUES 1-265
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Other Details: ADP
    Strain: K12
    Synonym: PSPF, PHAGE SHOCK PROTEIN F

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:9 , PHE A:15 , GLY A:39 , THR A:40 , GLY A:41 , LYS A:42 , GLU A:43 , LEU A:44 , ILE A:226 , ARG A:227 , HOH A:2110 , HOH A:2190 , HOH A:2191 , HOH A:2192 , HOH A:2193 , HOH A:2195 , HOH A:2196BINDING SITE FOR RESIDUE ADP A 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C98)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2C98)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C98)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SIGMA54_INTERACT_4PS50045 Sigma-54 interaction domain profile.PSPF_ECOLI8-238  1A:8-238
2SIGMA54_INTERACT_2PS00676 Sigma-54 interaction domain ATP-binding region B signature.PSPF_ECOLI94-109  1A:94-109
3SIGMA54_INTERACT_3PS00688 Sigma-54 interaction domain C-terminal part signature.PSPF_ECOLI222-231  1A:222-231

(-) Exons   (0, 0)

(no "Exon" information available for 2C98)

(-) 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:245
 aligned with PSPF_ECOLI | P37344 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:251
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257 
           PSPF_ECOLI     8 LLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNENLLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATAPMMVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRADLLDRLAFDVVQLPPLRERESDIMLMAEYFAIQMCREIKLPLFPGFTERARETLLNYRWPGNIRELKNVVERSVYRHGTSDYPLDDIIIDPFKRR 258
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2c98A01 A:8-179 P-loop containing nucleotide triphosphate hydrolases                                                                                                        2c98A02 A:180-258  [code=1.10.8.60, no name defined]                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhhee.------..ee.hhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhee........ee...eeeeee..hhhhhhhh...hhhhhhhhh.eeee..hhhhh.hhhhhhhhhhhhhhhhhh........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) SIGMA54_INTERACT_4  PDB: A:8-238 UniProt: 8-238                                                                                                                                                                                        -------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------SIGMA54_INTERACT----------------------------------------------------------------------------------------------------------------SIGMA54_IN--------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c98 A   8 LLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNENLLDSELFGHEA------QKRHPGRFERADGGTLFLDELATAPMMVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRADLLDRLAFDVVQLPPLRERESDIMLMAEYFAIQMCREIKLPLFPGFTERARETLLNYRWPGNIRELKNVVERSVYRHGTSDYPLDDIIIDPFKRR 258
                                    17        27        37        47        57        67        77    |    - |      97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257 
                                                                                                     82     89
   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 2C98)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C98)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PSPF_ECOLI | P37344)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
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:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases 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.

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  2c98
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 Related Entries

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

UniProtKB/Swiss-Prot
        PSPF_ECOLI | P37344: 2bjv 2bjw 2c96 2c99 2c9c 2vii 4qnm 4qnr 4qos 5nss

(-) Related Entries Specified in the PDB File

2bjv CRYSTAL STRUCTURE OF PSPF(1-275) R168A MUTANT
2bjw PSPF AAA DOMAIN
2c96 STRUCTURAL BASIS OF THE NUCLEOTIDE DRIVEN CONFORMATIONAL CHANGES IN THE AAA DOMAIN OF TRANSCRIPTION ACTIVATOR PSPF
2c99 STRUCTURAL BASIS OF THE NUCLEOTIDE DRIVEN CONFORMATIONAL CHANGES IN THE AAA DOMAIN OF TRANSCRIPTION ACTIVATOR PSPF
2c9c STRUCTURAL BASIS OF THE NUCLEOTIDE DRIVEN CONFORMATIONAL CHANGES IN THE AAA DOMAIN OF TRANSCRIPTION ACTIVATOR PSPF