1B9N - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

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 :   2.09

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)

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

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	NI	1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:139 , HIS A:140 , HIS A:146 , ASP A:148	BINDING SITE FOR RESIDUE NI A 263

(no "SS Bond" information available for 1B9N)

(no "Cis Peptide Bond" information available for 1B9N)

(no "SAP(SNP)/Variant" information available for 1B9N)

(no "PROSITE Motif" information available for 1B9N)

(no "Exon" information available for 1B9N)

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:264
                              1                                                                                                                                                                                                                                                                     
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258    
           MODE_ECOLI     - --MQAEILLTLKLQQKLFADPRRISLLKHIALSGSISQGAKDAGISYKSAWDAINEMNQLSEHILVERATGGKGGGGAVLTRYGQRLIQLYDLLAQIQQKAFDVLSDDDALPLNSLLAAISRFSLQTSARNQWFGTITARDHDDVQQHVDVLLADGKTRLKVAITAQSGARLGLDEGKEVLILLKAPWVGITQDEAVAQNADNQLPGIISHIERGAEQCEVLMALPDGQTLCATVPVNEATSLQQGQNVTAYFNADSVIIATLC 262
               SCOP domains d1b9na1 A:-2-126 N-terminal domain of molybdate-dependent transcriptio      nal regulator ModE                                  d1b9na3 A:127-199                                                        d1b9na4 A:200-262                                               SCOP domains
               CATH domains 1b9nA01 A:-2-106 'winged helix' repressor DNA binding domain                                                1b9nA02 A:107-181,A:253-262  [code=2.40.50.100, no name defined]           1b9nA03 A:182-252  [code=2.40.50.100, no name defined]                 1b9nA02    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eee..eeee.hhhhhhhhhhhhh..hhhhhhhh...hhhhhhhhhhhhhhh....eee..------.eee.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh........eeeeeee.........eeeee......eeeee..hhhhhh.......eeeee..hhh.eee..hhhhh...eeeeeeeeeee....eeeeeee.....eeeeeee.hhh.......eeeeee.hhh.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1b9n A  -2 SHMQAEILLTLKLQQKLFADPRRISLLKHIALSGSISQGAKDAGISYKSAWDAINEMNQLSEHILVERAT------GAVLTRYGQRLIQLYDLLAQIQQKAFDVLSDDDALPLNSLLAAISRFSLQTSARNQWFGTITARDHDDVQQHVDVLLADGKTRLKVAITAQSGARLGLDEGKEVLILLKAPWVGITQDEAVAQNADNQLPGIISHIERGAEQCEVLMALPDGQTLCATVPVNEATSLQQGQNVTAYFNADSVIIATLC 262
                             ||      8        18        28        38        48        58        68      | 78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258    
                             ||                                                                 68     75                                                                                                                                                                                           
                            -1|                                                                                                                                                                                                                                                                     
                              1

Chain B from PDB  Type:PROTEIN  Length:245
 aligned with MODE_ECOLI | P0A9G8 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260  
           MODE_ECOLI     1 MQAEILLTLKLQQKLFADPRRISLLKHIALSGSISQGAKDAGISYKSAWDAINEMNQLSEHILVERATGGKGGGGAVLTRYGQRLIQLYDLLAQIQQKAFDVLSDDDALPLNSLLAAISRFSLQTSARNQWFGTITARDHDDVQQHVDVLLADGKTRLKVAITAQSGARLGLDEGKEVLILLKAPWVGITQDEAVAQNADNQLPGIISHIERGAEQCEVLMALPDGQTLCATVPVNEATSLQQGQNVTAYFNADSVIIATLC 262
               SCOP domains d1b9nb1 B:1-126 N-terminal domain of molybdate-dependent transcri          ptional regulator ModE                             d1b9nb3 B:1       27-199                                                 d1b9nb4 B:200-262                                               SCOP domains
               CATH domains 1b9nB01 B:1-113 'winged helix' repressor DNA binding domain                                                      1b9nB02 B:114-181,B:253-       260  [code=2.40.50.100, no name defin1b9nB03 B:182-252  [code=2.40.50.100, no name defined]                 1b9nB02 -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eeee.hhhhhhhhhhhhh..hhhhhhhh...hhhhhhhhhhhhhhh......----------....hhhhhhhhhhhhhhhhhhhhhhhh..........hhhh...........eeeeeee..-------.eeeeee.....eeeee..hhhhhhh......eeeeee.hhh.eee..hhhhhh..eeeeeeeeeeee...eeeeeeee....eeeeeeehhh........eeeeee.hhh.eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b9n B   1 MQAEILLTLKLQQKLFADPRRISLLKHIALSGSISQGAKDAGISYKSAWDAINEMNQLSEHILVE----------AVLTRYGQRLIQLYDLLAQIQQKAFDVLSDDDALPLNSLLAAISRFSLQTSARNQWFGTITA-------QHVDVLLADGKTRLKVAITAQSGARLGLDEGKEVLILLKAPWVGITQDEAVAQNADNQLPGIISHIERGAEQCEVLMALPDGQTLCATVPVNEATSLQQGQNVTAYFNADSVIIATLC 262
                                    10        20        30        40        50        60    |    -     |  80        90       100       110       120       130      |  -    |  150       160       170       180       190       200       210       220       230       240       250       260  
                                                                                           65         76                                                          137     145

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

Escherichia coli. Organism_taxid: 562. (15)

1a	1b9nA01	A:-2-106
1b	1b9nB01	B:1-113

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: [code=2.40.50.100, no name defined] (113)

Escherichia coli. Organism_taxid: 562. (5)

2a	1b9nA02	A:107-181,A:253-262
2b	1b9nA03	A:182-252
2c	1b9nB03	B:182-252
2d	1b9nB02	B:114-181,B:253-260

(no "Pfam Domain" information available for 1B9N)

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.

Asymmetric/Biological Unit
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(no "Related Entries Specified in the PDB File" available for 1B9N)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (2, 6)

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