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(-) Description

Title :  RE-ENGINEERING TOPOLOGY OF THE HOMODIMERIC ROP PROTEIN INTO A SINGLE-CHAIN 4-HELIX BUNDLE
 
Authors :  M. Sagermann, S. C. Emery, C. Sander
Date :  26 Jan 05  (Deposition) - 15 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein Design, Re-Engineering Of Topology, Four-Helix Bundle, Replication Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sagermann, S. C. Emery, C. Sander
Re-Engineering Topology Of The Homodimeric Rop Protein Into A Single-Chain 4-Helix Bundle.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REGULATORY PROTEIN ROP
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI K12
    Expression System Plasmid: PEX70
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Expression System Vector Type: PLASMID
    Gene: ROP
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: THE GENE FOR LMROP2 WAS ARTIFICIALLY ASSEMBLED USING CASSETTE MUTAGENESIS AND CLONED INTO THE EXPRESSION VECTOR
    Synonym: RNA ONE MODULATOR, ROM

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:42 , ASP A:46 , HIS B:42 , ASP B:46BINDING SITE FOR RESIDUE ZN A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YO7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YO7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YO7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YO7)

(-) Exons   (0, 0)

(no "Exon" information available for 1YO7)

(-) Sequences/Alignments

Asymmetric 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:120
 aligned with ROP_ECOLX | P03051 from UniProtKB/Swiss-Prot  Length:63

    Alignment length:120
                                                                                                  63                                                
                                                                                      60        61 |                                                
                                    10        20        30        40        50        60        61 |       -         -         -         -         -
            ROP_ECOLX     1 MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHADELYRSCLARFGDDG---------ENL------------------------------------------------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 1yo7A00 A:1-120 de novo design (two linked rop proteins)                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1yo7 A   1 MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHADELYRSCLASFKKNGQIDEQADICESLHDHADELYRSCLARFGGSKQEKTALNMARFIRSQTLTLLEKLNELAKG 120
                                    10        20        30        40        50        60        70        80        90       100       110       120


Chain B from PDB  Type:PROTEIN  Length:120
 aligned with ROP_ECOLX | P03051 from UniProtKB/Swiss-Prot  Length:63

    Alignment length:120
                                                                                                  63                                                
                                                                                      60        61 |                                                
                                    10        20        30        40        50        60        61 |       -         -         -         -         -
            ROP_ECOLX     1 MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHADELYRSCLARFGDDG---------ENL------------------------------------------------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 1yo7B00 B:1-120 de novo design (two linked rop proteins)                                                                 CATH domains
           Pfam domains (1) Rop-1yo7B01 B:1-56                                      ---------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) Rop-1yo7B02 B:1-56                                      ---------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1yo7 B   1 MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHADELYRSCLASFKKNGQIDEQADICESLHDHADELYRSCLARFGGSKQEKTALNMARFIRSQTLTLLEKLNELAKG 120
                                    10        20        30        40        50        60        70        80        90       100       110       120
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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  (0, 0)

(no "SCOP Domain" information available for 1YO7)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Rop] (7)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ROP_ECOLX | P03051)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        ROP_ECOLX | P03051: 1b6q 1f4m 1f4n 1gmg 1gto 1nkd 1qx8 1rop 1rpo 1rpr 2ghy 2ijh 2iji 2ijj 2ijk 3k79 4do2

(-) Related Entries Specified in the PDB File

1rop REPRESSOR OF PRIMER AT 1.7 A RESOLUTION.