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(-) Description

Title :  CRYSTAL STRUCTURE OF A TWO-DOMAIN IDER-DNA COMPLEX CRYSTAL FORM II
 
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 :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Dna-Binding Protein, Transcription/Dna Complex (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 - MBTA/MBTB OPERATOR STRAND 1
    Chains: E
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - MBTA/MBTB OPERATOR STRAND 2
    Chains: F
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - IRON-DEPENDENT REPRESSOR IDER
    Chains: A, B, C, D
    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

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 22)

Asymmetric/Biological Unit (2, 22)
No.NameCountTypeFull Name
1ACT10Ligand/IonACETATE ION
2NI12Ligand/IonNICKEL (II) ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:79 , GLU A:83 , HIS A:98 , ACT A:2001BINDING SITE FOR RESIDUE NI A 1001
02AC2SOFTWAREMET A:10 , CYS A:102 , GLU A:105 , HIS A:106BINDING SITE FOR RESIDUE NI A 1002
03AC3SOFTWAREHIS A:61 , GLU A:63 , ACT A:2002 , ACT A:2003BINDING SITE FOR RESIDUE NI A 1003
04AC4SOFTWAREHIS B:79 , GLU B:83 , HIS B:98 , ACT B:2001BINDING SITE FOR RESIDUE NI B 1001
05AC5SOFTWAREMET B:10 , CYS B:102 , GLU B:105 , HIS B:106BINDING SITE FOR RESIDUE NI B 1002
06AC6SOFTWAREASP B:59 , HIS B:61 , GLU B:63 , ACT B:2002BINDING SITE FOR RESIDUE NI B 1003
07AC7SOFTWAREHIS C:79 , GLU C:83 , HIS C:98 , ACT C:2001BINDING SITE FOR RESIDUE NI C 1001
08AC8SOFTWAREMET C:10 , CYS C:102 , GLU C:105 , HIS C:106 , HOH C:2007BINDING SITE FOR RESIDUE NI C 1002
09AC9SOFTWAREASP C:59 , HIS C:61 , GLU C:63 , ACT C:2002 , ACT C:2003BINDING SITE FOR RESIDUE NI C 1003
10BC1SOFTWAREHIS D:79 , GLU D:83 , HIS D:98 , ACT D:2001BINDING SITE FOR RESIDUE NI D 1001
11BC2SOFTWAREMET D:10 , ARG D:13 , CYS D:102 , GLU D:105 , HIS D:106BINDING SITE FOR RESIDUE NI D 1002
12BC3SOFTWAREASP D:59 , HIS D:61 , GLU D:63 , ACT D:2002BINDING SITE FOR RESIDUE NI D 1003
13BC4SOFTWAREHIS A:79 , GLU A:83 , HIS A:98 , ASN A:130 , NI A:1001BINDING SITE FOR RESIDUE ACT A 2001
14BC5SOFTWAREHIS A:61 , GLU A:63 , NI A:1003BINDING SITE FOR RESIDUE ACT A 2002
15BC6SOFTWAREASP A:59 , HIS A:61 , GLU A:63 , NI A:1003BINDING SITE FOR RESIDUE ACT A 2003
16BC7SOFTWAREHIS B:79 , GLU B:83 , HIS B:98 , ASN B:130 , NI B:1001BINDING SITE FOR RESIDUE ACT B 2001
17BC8SOFTWAREHIS B:61 , GLU B:63 , NI B:1003BINDING SITE FOR RESIDUE ACT B 2002
18BC9SOFTWAREHIS C:79 , ARG C:80 , GLU C:83 , HIS C:98 , ASN C:130 , NI C:1001BINDING SITE FOR RESIDUE ACT C 2001
19CC1SOFTWAREASP A:88 , HIS C:61 , GLU C:63 , NI C:1003BINDING SITE FOR RESIDUE ACT C 2002
20CC2SOFTWAREASP C:59 , GLU C:63 , NI C:1003BINDING SITE FOR RESIDUE ACT C 2003
21CC3SOFTWAREHIS D:79 , GLU D:83 , HIS D:98 , NI D:1001BINDING SITE FOR RESIDUE ACT D 2001
22CC4SOFTWAREASP D:59 , HIS D:61 , GLU D:63 , NI D:1003BINDING SITE FOR RESIDUE ACT D 2002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IT0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IT0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IT0)

(-) PROSITE Motifs  (1, 4)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2IT0)

(-) 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:145
 aligned with IDER_MYCTO | P9WMH0 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152 
           IDER_MYCTO     3 ELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGVGPEPGADDANLVR 153
               SCOP domains d2it0a1 A:3-64 Iron-dependent regulator IdeR                  d2it0a2 A:65-147 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: A:4-65 UniProt: 4-65                           ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2it0 A   3 ELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGVASE------NLYF 147
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142|      146 
                                                                                                                                                                      143    144   


Chain A from PDB  Type:PROTEIN  Length:145
 aligned with IDER_MYCTU | P9WMH1 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152 
           IDER_MYCTU     3 ELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGVGPEPGADDANLVR 153
               SCOP domains d2it0a1 A:3-64 Iron-dependent regulator IdeR                  d2it0a2 A:65-147 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: A:4-65 UniProt: 4-65                           ---------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2it0 A   3 ELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGVASE------NLYF 147
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142|      146 
                                                                                                                                                                      143    144   


Chain A from PDB  Type:PROTEIN  Length:145
 aligned with LDT5_MYCTU | P9WKV3 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:269
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363         
           LDT5_MYCTU   104 KVVAGAYSRDRTIYTITEPLGYDTTYTWSGSAVGHDGKAVPVAGKFTTVAPVKTINAGFQLADGQTVGIAAPVIIQFDSPISDKAAVERALTVTTDPPVEGGWAWLPDEAQGARVHWRPREYYPAGTTVDVDAKLYGLPFGDGAYGAQDMSLHFQIGRRQVVKAEVSSHRIQVVTDAGVIMDFPCSYGEADLARNVTRNGIHVVTEKYSDFYMSNPAAGYSHIHERWAVRISNNGEFIHANPMSAGAQGNSNVTNGCINLSTENAEQYY 372
               SCOP domains d2it0a1 A:3-64 Iro                 n-           dependent        regulator IdeR                                                                           d2it0a2 A:65-147 Iron-depen dent regulat     or                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh-----------------h.-----------...hhhhhh-------hhh..hhhhhhhhhhhhhhh..ee----------e..-----------------------------------------------...eeehhhhhhhhhhhhhhhhhhhhhhhhh..-.hhhhhhhhhhh-----hh...hhhh----------------hhhhhhhh..-------....-.....--..hhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2it0 A   3 ELVDTTEMYLRTIYDLEE-----------------EG-----------VTPLRARIA-------ERLDQSGPTVSQTVSRMERDGLLR----------VAG-----------------------------------------------DRHLELTEKGRALAIAVMRKHRLAERLLVDVIG-LPWEEVHAEACR-----WEHVMSEDV----------------ERRLVKVLNN-------PTTS-PFGNP--IPGLVELGVASENLYF 147
                                    12       | -         -     ||  -        24      |  -    |   37        47       | -        57|        -         -         -         -        60        70        80        90| |     99   |   104       | -         -    |  118   |     - |  | |130|  |   138         
                                            20                21|          23      31      32                     55         56 |                                              59                              91 |        103   104     112              113      122     123  | | 131  |               
                                                               22                                                              58                                                                                92                                                           126 |    132               
                                                                                                                                                                                                                                                                                127                      


Chain B from PDB  Type:PROTEIN  Length:145
 aligned with IDER_MYCTO | P9WMH0 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152 
           IDER_MYCTO     3 ELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGVGPEPGADDANLVR 153
               SCOP domains d2it0b1 B:3-64 Iron-dependent regulator IdeR                  d2it0b2 B:65-147 Iron-dependent regulator                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...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
                 2it0 B   3 ELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGVASE------NLYF 147
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142|      146 
                                                                                                                                                                      143    144   


Chain B from PDB  Type:PROTEIN  Length:145
 aligned with IDER_MYCTU | P9WMH1 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152 
           IDER_MYCTU     3 ELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGVGPEPGADDANLVR 153
               SCOP domains d2it0b1 B:3-64 Iron-dependent regulator IdeR                  d2it0b2 B:65-147 Iron-dependent regulator                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...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
                 2it0 B   3 ELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELGVASE------NLYF 147
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142|      146 
                                                                                                                                                                      143    144   


Chain B from PDB  Type:PROTEIN  Length:145
 aligned with LDT5_MYCTU | P9WKV3 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:269
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363         
           LDT5_MYCTU   104 KVVAGAYSRDRTIYTITEPLGYDTTYTWSGSAVGHDGKAVPVAGKFTTVAPVKTINAGFQLADGQTVGIAAPVIIQFDSPISDKAAVERALTVTTDPPVEGGWAWLPDEAQGARVHWRPREYYPAGTTVDVDAKLYGLPFGDGAYGAQDMSLHFQIGRRQVVKAEVSSHRIQVVTDAGVIMDFPCSYGEADLARNVTRNGIHVVTEKYSDFYMSNPAAGYSHIHERWAVRISNNGEFIHANPMSAGAQGNSNVTNGCINLSTENAEQYY 372
               SCOP domains d2it0b1 B:3-64 Iro                 n-           dependent        regulator IdeR                                                                           d2it0b2 B:65-147 Iron-depen dent regulat     or                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh-----------------hh-----------...hhhhhh-------hhh..hhhhhhhhhhhhhhh..ee----------e..-----------------------------------------------...eeehhhhhhhhhhhhhhhhhhhhhhhhh..-.hhhhhhhhhhh-----hh...hhhh----------------hhhhhhhh..-------....-.....--..hhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2it0 B   3 ELVDTTEMYLRTIYDLEE-----------------EG-----------VTPLRARIA-------ERLDQSGPTVSQTVSRMERDGLLR----------VAG-----------------------------------------------DRHLELTEKGRALAIAVMRKHRLAERLLVDVIG-LPWEEVHAEACR-----WEHVMSEDV----------------ERRLVKVLNN-------PTTS-PFGNP--IPGLVELGVASENLYF 147
                                    12       | -         -     ||  -        24      |  -    |   37        47       | -        57|        -         -         -         -        60        70        80        90| |     99   |   104       | -         -    |  118   |     - |  | |130|  |   138         
                                            20                21|          23      31      32                     55         56 |                                              59                              91 |        103   104     112              113      122     123  | | 131  |               
                                                               22                                                              58                                                                                92                                                           126 |    132               
                                                                                                                                                                                                                                                                                127                      


Chain C from PDB  Type:PROTEIN  Length:137
 aligned with IDER_MYCTO | P9WMH0 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:137
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       
           IDER_MYCTO     3 ELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELG 139
               SCOP domains d2it0c1 C:3-64 Iron-dependent regulator IdeR                  d2it0c2 C:65-139 Iron-dependent regulator                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhh............hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HTH_DTXR  PDB: C:4-65 UniProt: 4-65                           -------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2it0 C   3 ELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELG 139
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       


Chain C from PDB  Type:PROTEIN  Length:137
 aligned with IDER_MYCTU | P9WMH1 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:137
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       
           IDER_MYCTU     3 ELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELG 139
               SCOP domains d2it0c1 C:3-64 Iron-dependent regulator IdeR                  d2it0c2 C:65-139 Iron-dependent regulator                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhh............hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -HTH_DTXR  PDB: C:4-65 UniProt: 4-65                           -------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2it0 C   3 ELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELG 139
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       


Chain C from PDB  Type:PROTEIN  Length:137
 aligned with LDT5_MYCTU | P9WKV3 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:261
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363 
           LDT5_MYCTU   104 KVVAGAYSRDRTIYTITEPLGYDTTYTWSGSAVGHDGKAVPVAGKFTTVAPVKTINAGFQLADGQTVGIAAPVIIQFDSPISDKAAVERALTVTTDPPVEGGWAWLPDEAQGARVHWRPREYYPAGTTVDVDAKLYGLPFGDGAYGAQDMSLHFQIGRRQVVKAEVSSHRIQVVTDAGVIMDFPCSYGEADLARNVTRNGIHVVTEKYSDFYMSNPAAGYSHIHERWAVRISNNGEFIHANPMSAGAQGNSNVTNGCINLS 364
               SCOP domains d2it0c1 C:3-64 Iro                 n-           dependent        regulator IdeR                                                                           d2it0c2 C:65-139 Iron-depen dent regulat     or                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh-----------------hh-----------...hhhhhh-------hhh..hhhhhhhhhhhhhhh..ee----------e..-----------------------------------------------...eeehhhhhhhhhhhhhhhhhhhhhhhhh..-.hhhhhhhhhhh-----hh...hhhh----------------hhhhhhhhh.-------....-.....--..hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2it0 C   3 ELVDTTEMYLRTIYDLEE-----------------EG-----------VTPLRARIA-------ERLDQSGPTVSQTVSRMERDGLLR----------VAG-----------------------------------------------DRHLELTEKGRALAIAVMRKHRLAERLLVDVIG-LPWEEVHAEACR-----WEHVMSEDV----------------ERRLVKVLNN-------PTTS-PFGNP--IPGLVELG 139
                                    12       | -         -     ||  -        24      |  -    |   37        47       | -        57|        -         -         -         -        60        70        80        90| |     99   |   104       | -         -    |  118   |     - |  | |130|  |   138 
                                            20                21|          23      31      32                     55         56 |                                              59                              91 |        103   104     112              113      122     123  | | 131  |       
                                                               22                                                              58                                                                                92                                                           126 |    132       
                                                                                                                                                                                                                                                                                127              


Chain D from PDB  Type:PROTEIN  Length:137
 aligned with IDER_MYCTO | P9WMH0 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:137
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       
           IDER_MYCTO     3 ELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELG 139
               SCOP domains d2it0d1 D:3-64 Iron-dependent regulator IdeR                  d2it0d2 D:65-139 Iron-dependent regulator                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh.............hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HTH_DTXR  PDB: D:4-65 UniProt: 4-65                           -------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2it0 D   3 ELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELG 139
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       


Chain D from PDB  Type:PROTEIN  Length:137
 aligned with IDER_MYCTU | P9WMH1 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:137
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       
           IDER_MYCTU     3 ELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELG 139
               SCOP domains d2it0d1 D:3-64 Iron-dependent regulator IdeR                  d2it0d2 D:65-139 Iron-dependent regulator                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh.............hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -HTH_DTXR  PDB: D:4-65 UniProt: 4-65                           -------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2it0 D   3 ELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLVELG 139
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       


Chain D from PDB  Type:PROTEIN  Length:137
 aligned with LDT5_MYCTU | P9WKV3 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:261
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363 
           LDT5_MYCTU   104 KVVAGAYSRDRTIYTITEPLGYDTTYTWSGSAVGHDGKAVPVAGKFTTVAPVKTINAGFQLADGQTVGIAAPVIIQFDSPISDKAAVERALTVTTDPPVEGGWAWLPDEAQGARVHWRPREYYPAGTTVDVDAKLYGLPFGDGAYGAQDMSLHFQIGRRQVVKAEVSSHRIQVVTDAGVIMDFPCSYGEADLARNVTRNGIHVVTEKYSDFYMSNPAAGYSHIHERWAVRISNNGEFIHANPMSAGAQGNSNVTNGCINLS 364
               SCOP domains d2it0d1 D:3-64 Iro                 n-           dependent        regulator IdeR                                                                           d2it0d2 D:65-139 Iron-depen dent regulat     or                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh-----------------hh-----------...hhhhhh-------hhhh.hhhhhhhhhhhhhhh..ee----------e..-----------------------------------------------...eeehhhhhhhhhhhhhhhhhhhhhhhhh..-.hhhhhhhhhhh-----hh...hhhh----------------hhhhhhhh..-------....-.....--..hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2it0 D   3 ELVDTTEMYLRTIYDLEE-----------------EG-----------VTPLRARIA-------ERLDQSGPTVSQTVSRMERDGLLR----------VAG-----------------------------------------------DRHLELTEKGRALAIAVMRKHRLAERLLVDVIG-LPWEEVHAEACR-----WEHVMSEDV----------------ERRLVKVLNN-------PTTS-PFGNP--IPGLVELG 139
                                    12       | -         -     ||  -        24      |  -    |   37        47       | -        57|        -         -         -         -        60        70        80        90| |     99   |   104       | -         -    |  118   |     - |  | |130|  |   138 
                                            20                21|          23      31      32                     55         56 |                                              59                              91 |        103   104     112              113      122     123  | | 131  |       
                                                               22                                                              58                                                                                92                                                           126 |    132       
                                                                                                                                                                                                                                                                                127              


Chain E from PDB  Type:DNA  Length:33
                                                                 
                 2it0 E   1 CCCTGTTAGCACAGGCTGCCCTAATTTTAGTGG  33
                                    10        20        30   


Chain F from PDB  Type:DNA  Length:33
                                                                 
                 2it0 F   1 CACTAAAATTAGGGCAGCCTGTGCTAACAGGGC  33
                                    10        20        30
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 8)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2IT0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IT0)

(-) Gene Ontology  (27, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (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,B,C,D   (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,C,D   (LDT5_MYCTU | P9WKV3)
molecular function
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IDER_MYCTO | P9WMH0: 1b1b 1fx7 1u8r 2isy 2isz
        IDER_MYCTU | P9WMH1: 1b1b 1fx7 1u8r 2isy 2isz
        LDT5_MYCTU | P9WKV3: 1u8r 2isz

(-) 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
2isy CRYSTAL STRUCTURE OF THE NICKEL-ACTIVATED TWO-DOMAIN IRON- DEPENDENT REGULATOR
2isz CRYSTAL STRUCTURE OF A TWO-DOMAIN IDER-DNA COMPLEX CRYSTAL FORM I