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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NICKEL-ACTIVATED TWO-DOMAIN IRON-DEPENDENT REGULATOR (IDER)
 
Authors :  G. Wisedchaisri, C. J. Chou, M. Wu, C. Roach, A. E. Rice, R. K. Holmes, C. Beeson, W. G. Hol
Date :  18 Oct 06  (Deposition) - 13 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna-Binding Protein, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Wisedchaisri, C. J. Chou, M. Wu, C. Roach, A. E. Rice, R. K. Holmes, C. Beeson, W. G. Hol
Crystal Structures, Metal Activation, And Dna-Binding Properties Of Two-Domain Ider From Mycobacterium Tuberculosis
Biochemistry V. 46 436 2007
PubMed-ID: 17209554  |  Reference-DOI: 10.1021/BI0609826
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IRON-DEPENDENT REPRESSOR IDER
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PAER36
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: IDER,DTXR
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CSO2Mod. Amino AcidS-HYDROXYCYSTEINE
2NI4Ligand/IonNICKEL (II) ION
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:79 , GLU A:83 , HIS A:98 , PO4 A:2001 , HOH A:2017 , HOH A:2020BINDING SITE FOR RESIDUE NI A 1001
2AC2SOFTWAREMET A:10 , CSO A:102 , GLU A:105 , HIS A:106 , HOH A:2043BINDING SITE FOR RESIDUE NI A 1002
3AC3SOFTWAREHIS B:79 , GLU B:83 , HIS B:98 , PO4 B:2001 , HOH B:2017 , HOH B:2046BINDING SITE FOR RESIDUE NI B 1001
4AC4SOFTWAREMET B:10 , CSO B:102 , GLU B:105 , HIS B:106 , HOH B:2013BINDING SITE FOR RESIDUE NI B 1002
5AC5SOFTWAREHIS A:79 , ARG A:80 , GLU A:83 , SER A:126 , PHE A:128 , ASN A:130 , NI A:1001 , HOH A:2017 , HOH A:2020 , HOH A:2041 , HOH A:2054BINDING SITE FOR RESIDUE PO4 A 2001
6AC6SOFTWAREHIS B:79 , ARG B:80 , GLU B:83 , SER B:126 , PHE B:128 , ASN B:130 , NI B:1001 , HOH B:2017 , HOH B:2042 , HOH B:2046BINDING SITE FOR RESIDUE PO4 B 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ISY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ISY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ISY)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_DTXRPS50944 DtxR-type HTH domain profile.IDER_MYCTO4-65
 		  2A:4-65
B:4-65
IDER_MYCTU4-65
 		  2A:4-65
B:4-65

(-) Exons   (0, 0)

(no "Exon" information available for 2ISY)

(-) 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:147
 aligned with IDER_MYCTO | P9WMH0 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:174
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171    
           IDER_MYCTO     2 NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGVGPEPGADDANLVRLTELPAGSPVAVVVRQLTEHVQ 175
               SCOP domains d2isya1 A:2-64 Iron-dependent regulator IdeR                   d2isya2 A:65-148 Iron-dependent regulator                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh.............hhhhhh.....---------------------------.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --HTH_DTXR  PDB: A:4-65 UniProt: 4-65                           -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2isy A   2 NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEAcRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGVASEN---------------------------LYFQ 148
                                    11        21        31        41        51        61        71        81        91       101|      111       121       131       141  |      -         -         -|   
                                                                                                                              102-CSO                                   144                         145   


Chain A from PDB  Type:PROTEIN  Length:147
 aligned with IDER_MYCTU | P9WMH1 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:174
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171    
           IDER_MYCTU     2 NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGVGPEPGADDANLVRLTELPAGSPVAVVVRQLTEHVQ 175
               SCOP domains d2isya1 A:2-64 Iron-dependent regulator IdeR                   d2isya2 A:65-148 Iron-dependent regulator                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh.............hhhhhh.....---------------------------.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) --HTH_DTXR  PDB: A:4-65 UniProt: 4-65                           -------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2isy A   2 NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEAcRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGVASEN---------------------------LYFQ 148
                                    11        21        31        41        51        61        71        81        91       101|      111       121       131       141  |      -         -         -|   
                                                                                                                              102-CSO                                   144                         145   


Chain B from PDB  Type:PROTEIN  Length:147
 aligned with IDER_MYCTO | P9WMH0 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:174
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171    
           IDER_MYCTO     2 NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGVGPEPGADDANLVRLTELPAGSPVAVVVRQLTEHVQ 175
               SCOP domains d2isyb1 B:2-64 Iron-dependent regulator IdeR                   d2isyb2 B:65-148 Iron-dependent regulator                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh.............hhhhhh.....---------------------------.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --HTH_DTXR  PDB: B:4-65 UniProt: 4-65                           -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2isy B   2 NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEAcRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGVASEN---------------------------LYFQ 148
                                    11        21        31        41        51        61        71        81        91       101|      111       121       131       141  |      -         -         -|   
                                                                                                                              102-CSO                                   144                         145   


Chain B from PDB  Type:PROTEIN  Length:147
 aligned with IDER_MYCTU | P9WMH1 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:174
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171    
           IDER_MYCTU     2 NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGVGPEPGADDANLVRLTELPAGSPVAVVVRQLTEHVQ 175
               SCOP domains d2isyb1 B:2-64 Iron-dependent regulator IdeR                   d2isyb2 B:65-148 Iron-dependent regulator                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh.............hhhhhh.....---------------------------.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) --HTH_DTXR  PDB: B:4-65 UniProt: 4-65                           -------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2isy B   2 NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEAcRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGVASEN---------------------------LYFQ 148
                                    11        21        31        41        51        61        71        81        91       101|      111       121       131       141  |      -         -         -|   
                                                                                                                              102-CSO                                   144                         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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ISY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ISY)

(-) Gene Ontology  (21, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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.

Chain A,B   (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.

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  2isy
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 Related Entries

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

UniProtKB/Swiss-Prot
        IDER_MYCTO | P9WMH0: 1b1b 1fx7 1u8r 2isz 2it0
        IDER_MYCTU | P9WMH1: 1b1b 1fx7 1u8r 2isz 2it0

(-) Related Entries Specified in the PDB File

1fx7 CRYSTAL STRUCTURE OF THE COBALT-ACTIVATED FULL-LENGTH IDER
1u8r CRYSTAL STRUCTURE OF A FULL-LENGTH IDER-DNA COMPLEX
2isz
2it0