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(-) Description

Title :  REGULATOR FROM ESCHERICHIA COLI
 
Authors :  D. R. Hall, D. G. Gourley, W. N. Hunter
Date :  12 Feb 99  (Deposition) - 15 Mar 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna-Binding, Gene Regulation, Winged Helix Turn Helix, Molybdate, Ob Fold, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. R. Hall, D. G. Gourley, G. A. Leonard, E. M. Duke, L. A. Anderson, D. H. Boxer, W. N. Hunter
The High-Resolution Crystal Structure Of The Molybdate-Dependent Transcriptional Regulator (Mode) From Escherichia Coli: A Novel Combination Of Domain Folds.
Embo J. V. 18 1435 1999
PubMed-ID: 10075916  |  Reference-DOI: 10.1093/EMBOJ/18.6.1435
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (MODE)
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2NI1Ligand/IonNICKEL (II) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:139 , HIS A:140 , HIS A:146 , ASP A:148 , HOH A:465BINDING SITE FOR RESIDUE NI A 263

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1B9M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1B9M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B9M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1B9M)

(-) Exons   (0, 0)

(no "Exon" information available for 1B9M)

(-) 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:258
 aligned with MODE_ECOLI | P0A9G8 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:263
                             1                                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259   
           MODE_ECOLI     - -MQAEILLTLKLQQKLFADPRRISLLKHIALSGSISQGAKDAGISYKSAWDAINEMNQLSEHILVERATGGKGGGGAVLTRYGQRLIQLYDLLAQIQQKAFDVLSDDDALPLNSLLAAISRFSLQTSARNQWFGTITARDHDDVQQHVDVLLADGKTRLKVAITAQSGARLGLDEGKEVLILLKAPWVGITQDEAVAQNADNQLPGIISHIERGAEQCEVLMALPDGQTLCATVPVNEATSLQQGQNVTAYFNADSVIIATLC 262
               SCOP domains d1b9ma1 A:-1-126 N-terminal domain of molybdate-dependent transcripti     onal regulator ModE                                  d1b9ma3 A:127-199                                                        d1b9ma4 A:200-262                                               SCOP domains
               CATH domains 1b9mA01 A:-1-106 'winged helix' repressor DNA binding domain                                               1b9mA02 A:107-181,A:253-258  [code=2.40.50.100, no name defined]           1b9mA03 A:182-252  [code=2.40.50.100, no name defined]                 1b9mA0---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee..eeee.hhhhhhhhhhhhh..hhhhhhhh...hhhhhhhhhhhhhhh....eee..-----..eee.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh.......eeeeeee..........eeeeee.....eeeee..hhhhhh.......eeeeee.hhh.eee..hhhhhh..eeeeeeeeeeee...eeeeeee.....eeeeeeehhhh.......eeeeee.hhh.eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b9m A  -1 HmQAEILLTLKLQQKLFADPRRISLLKHIALSGSISQGAKDAGISYKSAWDAINEmNQLSEHILVERAT-----GGAVLTRYGQRLIQLYDLLAQIQQKAFDVLSDDDALPLNSLLAAISRFSLQTSARNQWFGTITARDHDDVQQHVDVLLADGKTRLKVAITAQSGARLGLDEGKEVLILLKAPWVGITQDEAVAQNADNQLPGIISHIERGAEQCEVLmALPDGQTLCATVPVNEATSLQQGQNVTAYFNADSVIIATLC 262
                            ||       9        19        29        39        49     |  59        |-    |   79        89        99       109       119       129       139       149       159       169       179       189       199       209       219 |     229       239       249       259   
                            ||                                                    55-MSE       68    74                                                                                                                                                221-MSE                                     
                           -1|                                                                                                                                                                                                                                                                     
                             1-MSE                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:247
 aligned with MODE_ECOLI | P0A9G8 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:263
                             1                                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259   
           MODE_ECOLI     - -MQAEILLTLKLQQKLFADPRRISLLKHIALSGSISQGAKDAGISYKSAWDAINEMNQLSEHILVERATGGKGGGGAVLTRYGQRLIQLYDLLAQIQQKAFDVLSDDDALPLNSLLAAISRFSLQTSARNQWFGTITARDHDDVQQHVDVLLADGKTRLKVAITAQSGARLGLDEGKEVLILLKAPWVGITQDEAVAQNADNQLPGIISHIERGAEQCEVLMALPDGQTLCATVPVNEATSLQQGQNVTAYFNADSVIIATLC 262
               SCOP domains d1b9mb1 B:-1-126 N-terminal domain of molybdate-dependent transcrip         tional regulator ModE                              d1b9mb3 B:1       27-199                                                 d1b9mb4 B:200-262                                               SCOP domains
               CATH domains 1b9mB01 B:-1-107 'winged helix' repressor DNA binding domain                                                1b9mB02 B:108-181,B:253-257  [       code=2.40.50.100, no name defined]   1b9mB03 B:182-252  [code=2.40.50.100, no name defined]                 1b9mB----- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee..eeee.hhhhhhhhhhhhh..hhhhhhhh...hhhhhhhhhhhhhhh.......---------....hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhh........eeeeeee..-------.eeeeee.....eeeee..hhhhhhh......eeeeee.hhh.eee..hhhhhh..eeeeeeeeeeee...eeeeeee.....eeeeeeehhh........eeeeee.hhh.eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b9m B  -1 HmQAEILLTLKLQQKLFADPRRISLLKHIALSGSISQGAKDAGISYKSAWDAINEmNQLSEHILVER---------AVLTRYGQRLIQLYDLLAQIQQKAFDVLSDDDALPLNSLLAAISRFSLQTSARNQWFGTITA-------QHVDVLLADGKTRLKVAITAQSGARLGLDEGKEVLILLKAPWVGITQDEAVAQNADNQLPGIISHIERGAEQCEVLmALPDGQTLCATVPVNEATSLQQGQNVTAYFNADSVIIATLC 262
                            ||       9        19        29        39        49     |  59      |  -      | 79        89        99       109       119       129       | -     | 149       159       169       179       189       199       209       219 |     229       239       249       259   
                           -1|                                                    55-MSE     66        76                                                          137     145                                                                         221-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  (2, 6)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B9M)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MODE_ECOLI | P0A9G8)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0030151    molybdenum ion binding    Interacting selectively and non-covalently with molybdenum (Mo) ions.
    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:0015689    molybdate ion transport    The directed movement of molybdate (MoO4 2-) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Molybdate is the bivalent anion derived from molybdic acid.
    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.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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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        MODE_ECOLI | P0A9G8: 1b9n 1h9r 1h9s 1o7l

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