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(-) Description

Title :  CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA ICLR
 
Authors :  Y. Kim, R. G. Zhang, A. Joachimiak, T. Skarina, A. Edwards, A. Savchenko, Midwest Center For Structural Genomics (Mcsg)
Date :  29 Aug 02  (Deposition) - 11 Sep 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Structural Genomics, Winged Helix-Turn-Helix, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. G. Zhang, Y. Kim, T. Skarina, S. Beasley, R. Laskowski, C. Arrowsmith, A. Edwards, A. Joachimiak, A. Savchenko
Crystal Structure Of Thermotoga Maritima 0065, A Member Of The Iclr Transcriptional Factor Family.
J. Biol. Chem. V. 277 19183 2002
PubMed-ID: 11877432  |  Reference-DOI: 10.1074/JBC.M112171200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ICLR TRANSCRIPTIONAL REGULATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR B:133 , CYS B:196 , SER B:213BINDING SITE FOR RESIDUE ZN B 401
2AC2SOFTWARETHR A:133 , ALA A:134 , ASP A:186 , CYS A:196BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWAREGLY A:68 , SER A:69 , ILE B:65 , GLY B:68 , SER B:69BINDING SITE FOR RESIDUE FMT A 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MKM)

(-) Sequences/Alignments

Asymmetric 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:246
 aligned with Q9WXS0_THEMA | Q9WXS0 from UniProtKB/TrEMBL  Length:246

    Alignment length:246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
         Q9WXS0_THEMA     1 MNTLKKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRYVPGYKLIEYGSFVLRRFNIRDIAHDHLVDIMKRTGETVHLILKDGFEGVYIDKVEGEQSIPMVSRLGMKVDLYSTASGKSILAFVPEKELKEYLKIVELKPKTPNTITNPRVLKRELEKIRKRGYAVDNEENEIGIMCVGVPIFDHNGYPVAGVSISGVARKFTEEKIEEYSDVLKEKAEEISRKLGY 246
               SCOP domains d1mkma1 A:1-75 Transcriptional regulator IclR, N-terminal domain           d1mkma2 A:76-246 Transcriptional regulator IclR, C-terminal domain                                                                                                          SCOP domains
               CATH domains 1mkmA01 A:1-60 'winged helix' repressor DNA binding domain  1mkmA02       1mkmA03 A:75-246  [code=3.30.450.40, no name defined]                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhh..eee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee...eeeeeeee..............eee...hhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh.eeee......eeeeeeeee.....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mkm A   1 MNTLKKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRYVPGYKLIEYGSFVLRRFNIRDIAHDHLVDIMKRTGETVHLILKDGFEGVYIDKVEGEQSIPMVSRLGMKVDLYSTASGKSILAFVPEKELKEYLKIVELKPKTPNTITNPRVLKRELEKIRKRGYAVDNEENEIGIMCVGVPIFDHNGYPVAGVSISGVARKFTEEKIEEYSDVLKEKAEEISRKLGY 246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      


Chain B from PDB  Type:PROTEIN  Length:247
 aligned with Q9WXS0_THEMA | Q9WXS0 from UniProtKB/TrEMBL  Length:246

    Alignment length:247
                             1                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       
         Q9WXS0_THEMA     - -MNTLKKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRYVPGYKLIEYGSFVLRRFNIRDIAHDHLVDIMKRTGETVHLILKDGFEGVYIDKVEGEQSIPMVSRLGMKVDLYSTASGKSILAFVPEKELKEYLKIVELKPKTPNTITNPRVLKRELEKIRKRGYAVDNEENEIGIMCVGVPIFDHNGYPVAGVSISGVARKFTEEKIEEYSDVLKEKAEEISRKLGY 246
               SCOP domains d1mkmb1 B:0-75 Transcriptional regulator IclR, N-terminal domain            d1mkmb2 B:76-246 Transcriptional regulator IclR, C-terminal domain                                                                                                          SCOP domains
               CATH domains 1mkmB01 B:0-75 'winged helix' repressor DNA binding domain                  1mkmB02 B:76-246  [code=3.30.450.40, no name defined]                                                                                                                       CATH domains
           Pfam domains (1) ---HTH_IclR-1mkmB03 B:3-53                            --------------------------------------------------------------IclR-1mkmB01 B:116-243                                                                                                          --- Pfam domains (1)
           Pfam domains (2) ---HTH_IclR-1mkmB04 B:3-53                            --------------------------------------------------------------IclR-1mkmB02 B:116-243                                                                                                          --- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhh..eee.....eee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeee..............eee...hhhhhhhhh..hhhhhhhhhhhh...........hhhhhhhhhhhhhhhh.eeee......eeeeeeeee.....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mkm B   0 HMNTLKKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRYVPGYKLIEYGSFVLRRFNIRDIAHDHLVDIMKRTGETVHLILKDGFEGVYIDKVEGEQSIPMVSRLGMKVDLYSTASGKSILAFVPEKELKEYLKIVELKPKTPNTITNPRVLKRELEKIRKRGYAVDNEENEIGIMCVGVPIFDHNGYPVAGVSISGVARKFTEEKIEEYSDVLKEKAEEISRKLGY 246
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239
   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 Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (3, 5)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: GAF (44)
(-)
Family: IclR (7)
(-)
Thermotoga maritima (1)
1aIclR-1mkmB01B:116-243
1bIclR-1mkmB02B:116-243
(-)
Clan: HTH (544)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9WXS0_THEMA | Q9WXS0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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