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Asym./Biol. Unit (Jmol Viewer)

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

Title :   IRON DEPENDENT REGULATOR

Authors :   E. Pohl, R. K. Holmes, W. G. Hol

Date :   19 Nov 98 (Deposition) - 03 Dec 99 (Release) - 02 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A

Keywords :   Ider, Iron Depedent Regulator, Mycobacterium Tuberculosis, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Pohl, R. K. Holmes, W. G. Hol
Crystal Structure Of The Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis Shows Both Metal Binding Sites Fully Occupied.
J. Mol. Biol. V. 285 1145 1999
PubMed-ID: 9887269 | Reference-DOI: 10.1006/JMBI.1998.2339

Molecule 1 - PROTEIN (IRON DEPENDENT REGULATOR)
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMTBKS
	Expression System Strain	:	DH5-ALPHA
	Expression System Taxid	:	562
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	IDER

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION
2	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:79 , GLU A:83 , HIS A:98 , SO4 A:303 , HOH A:425	BINDING SITE FOR RESIDUE ZN A 301
2	AC2	SOFTWARE	GLU A:3 , MET A:10 , CYS A:102 , GLU A:105 , HIS A:106	BINDING SITE FOR RESIDUE ZN A 302
3	AC3	SOFTWARE	ASP A:17 , MET A:76 , HIS A:79 , ARG A:80 , HIS A:98 , ASN A:130 , ZN A:301	BINDING SITE FOR RESIDUE SO4 A 303

(no "SS Bond" information available for 1B1B)

(no "Cis Peptide Bond" information available for 1B1B)

(no "SAP(SNP)/Variant" information available for 1B1B)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_DTXR	PS50944	DtxR-type HTH domain profile.	IDER_MYCTO	4-65	1	A:4-65
1	HTH_DTXR	PS50944	DtxR-type HTH domain profile.	IDER_MYCTU	4-65	1	A:4-65

(no "Exon" information available for 1B1B)

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
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Chain A from PDB  Type:PROTEIN  Length:140
 aligned with IDER_MYCTO | P9WMH0 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
           IDER_MYCTO     1 MNELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGV 140
               SCOP domains d1b1ba1 A:1-64 Iron-dependent regulator IdeR                    d1b1ba2 A:65-140 Iron-dependent regulator                                    SCOP domains
               CATH domains --1b1bA01 A:3-75 'winged helix' repressor DNA binding domain               1b1bA02 A:76-136 Diphtheria Toxin Repressor, domain 2        ---- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhh...eee.....eeehhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh...hhhhhhhhhhhh.............hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HTH_DTXR  PDB: A:4-65 UniProt: 4-65                           --------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b1b A   1 MNELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGV 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain A from PDB  Type:PROTEIN  Length:140
 aligned with IDER_MYCTU | P9WMH1 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
           IDER_MYCTU     1 MNELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGV 140
               SCOP domains d1b1ba1 A:1-64 Iron-dependent regulator IdeR                    d1b1ba2 A:65-140 Iron-dependent regulator                                    SCOP domains
               CATH domains --1b1bA01 A:3-75 'winged helix' repressor DNA binding domain               1b1bA02 A:76-136 Diphtheria Toxin Repressor, domain 2        ---- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhh...eee.....eeehhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh...hhhhhhhhhhhh.............hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---HTH_DTXR  PDB: A:4-65 UniProt: 4-65                           --------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b1b A   1 MNELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGV 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

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 '\|'

(no "Pfam Domain" information available for 1B1B)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (IDER_MYCTO | P9WMH0)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	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.
	GO:0046914	transition metal ion binding	Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A (IDER_MYCTU | P9WMH1)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046870	cadmium ion binding	Interacting selectively and non-covalently with cadmium (Cd) ions.
	GO:0050897	cobalt ion binding	Interacting selectively and non-covalently with a cobalt (Co) ion.
	GO:0008198	ferrous iron binding	Interacting selectively and non-covalently with ferrous iron, Fe(II).
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0016151	nickel cation binding	Interacting selectively and non-covalently with nickel (Ni) cations.
	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:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	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.
	GO:0046914	transition metal ion binding	Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0019540	siderophore biosynthetic process from catechol	The chemical reactions and pathways resulting in the formation of a siderophore from other compounds, including catechol.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	IDER_MYCTO \| P9WMH0	:	1fx7 1u8r 2isy 2isz 2it0
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