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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BEF3-ACTIVATED RECEIVER DOMAIN OF REDOX RESPONSE REGULATOR ARCA
 
Authors :  A. Toro-Roman, T. R. Mack, A. M. Stock
Date :  18 Sep 04  (Deposition) - 17 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Two-Component System; Gene Regulation; Transcription Factor; Anoxic Redox Control; Doubly Wound Five-Stranded Beta/Alpha Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Toro-Roman, T. R. Mack, A. M. Stock
Structural Analysis And Solution Studies Of The Activated Regulatory Domain Of The Response Regulator Arca: A Symmetric Dimer Mediated By The Alpha4-Beta5-Alpha5 Face
J. Mol. Biol. V. 349 11 2005
PubMed-ID: 15876365  |  Reference-DOI: 10.1016/J.JMB.2005.03.059
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AEROBIC RESPIRATION CONTROL PROTEIN ARCA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEF29 (PJES307 DERIVATIVE)
    Expression System Strain: B834(DE3)PLYSS AND BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RECEIVER DOMAIN
    Gene: ARCA, DYE, FEXA, SFRA, SEG, MSP, CPXC
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: REDOX RESPONSE REGULATOR ARCA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric/Biological Unit (5, 16)
No.NameCountTypeFull Name
1BEF3Ligand/IonBERYLLIUM TRIFLUORIDE ION
2BF21Ligand/IonBERYLLIUM DIFLUORIDE
3BF41Ligand/IonBERYLLIUM TETRAFLUORIDE ION
4MG2Ligand/IonMAGNESIUM ION
5MSE9Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:11 , ASP A:54 , ASN A:56 , BEF A:2001 , HOH A:2016 , HOH A:2047BINDING SITE FOR RESIDUE MG A 1001
2AC2SOFTWAREASP B:11 , ASP B:54 , ASN B:56 , BEF B:2002 , HOH B:4008 , HOH B:4052BINDING SITE FOR RESIDUE MG B 1002
3AC3SOFTWAREASP A:54 , ILE A:55 , ASN A:56 , THR A:81 , GLY A:82 , LYS A:103 , MG A:1001 , HOH A:2016 , HOH A:2047BINDING SITE FOR RESIDUE BEF A 2001
4AC4SOFTWAREASP B:54 , ILE B:55 , ASN B:56 , THR B:81 , GLY B:82 , LYS B:103 , MG B:1002 , HOH B:4008 , HOH B:4052BINDING SITE FOR RESIDUE BEF B 2002
5AC5SOFTWAREARG A:70 , ASN A:74BINDING SITE FOR RESIDUE BEF B 2003
6AC6SOFTWAREARG B:70 , ASN B:74BINDING SITE FOR RESIDUE BF2 B 4001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XHF)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:103 -Pro A:104
2Lys B:103 -Pro B:104

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XHF)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RESPONSE_REGULATORYPS50110 Response regulatory domain profile.ARCA_ECOLI5-118
 		  2A:5-118
B:5-118

(-) Exons   (0, 0)

(no "Exon" information available for 1XHF)

(-) 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:121
 aligned with ARCA_ECOLI | P0A9Q1 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
           ARCA_ECOLI     2 QTPHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSEYDINLVIMDINLPGKNGLLLARELREQANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSRTM 122
               SCOP domains d1xhfa_ A: automated matches                                                                                              SCOP domains
               CATH domains 1xhfA00 A:2-121  [code=3.40.50.2300, no name defined]                                                                   - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---RESPONSE_REGULATORY  PDB: A:5-118 UniProt: 5-118                                                                  ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xhf A   2 QTPHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEmHQILSEYDINLVImDINLPGKNGLLLARELREQANVALmFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSRTm 122
                                    11        21        31       |41        51 |      61        71      | 81        91       101       111       121|
                                                                39-MSE        53-MSE                   78-MSE                                     122-MSE


Chain B from PDB  Type:PROTEIN  Length:122
 aligned with ARCA_ECOLI | P0A9Q1 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
           ARCA_ECOLI     1 MQTPHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSEYDINLVIMDINLPGKNGLLLARELREQANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSRTM 122
               SCOP domains d1xhfb_ B: automated matches                                                                                               SCOP domains
               CATH domains -1xhfB00 B:2-121  [code=3.40.50.2300, no name defined]                                                                   - CATH domains
           Pfam domains (1) -----Response_reg-1xhfB01 B:6-115                                                                                  ------- Pfam domains (1)
           Pfam domains (2) -----Response_reg-1xhfB02 B:6-115                                                                                  ------- Pfam domains (2)
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----RESPONSE_REGULATORY  PDB: B:5-118 UniProt: 5-118                                                                  ---- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xhf B   1 mQTPHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEmHQILSEYDINLVImDINLPGKNGLLLARELREQANVALmFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSRTm 122
                            |       10        20        30        40        50  |     60        70       |80        90       100       110       120 |
                            |                                    39-MSE        53-MSE                   78-MSE                                     122-MSE
                            1-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  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: CheY (97)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ARCA_ECOLI | P0A9Q1)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0000156    phosphorelay response regulator activity    Responds to a phosphorelay sensor to initiate a change in cell state or activity. The activity of the response regulator is regulated by transfer of a phosphate from a histidine residue in the sensor, to an aspartate residue in the response regulator. Many but not all response regulators act as transcriptional regulators to elicit a response.
    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: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: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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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        ARCA_ECOLI | P0A9Q1: 1xhe

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1xhe