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(-) Description

Title :  CRYSTAL STRUCTURE OF A MUTANT IHF (BETAE44A) COMPLEXED WITH A VARIANT H' SITE (T44A)
 
Authors :  T. W. Lynch, E. K. Read, A. N. Mattis, J. F. Gardner, P. A. Rice
Date :  25 Mar 03  (Deposition) - 15 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Protein-Dna Recognition, Indirect Readout, Ihf, Dna Bending, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. W. Lynch, E. K. Read, A. N. Mattis, J. F. Gardner, P. A. Rice
Integration Host Factor: Putting A Twist On Protein-Dna Recognition
J. Mol. Biol. V. 330 493 2003
PubMed-ID: 12842466  |  Reference-DOI: 10.1016/S0022-2836(03)00529-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHAGE LAMBDA H' SITE
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'- D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3'
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'- D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*AP*GP*CP*AP*CP *C)-3'
    Chains: E
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - INTEGRATION HOST FACTOR ALPHA-SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: IHF-ALPHA
 
Molecule 5 - INTEGRATION HOST FACTOR BETA-SUBUNIT
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: IHF-BETA

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1OUZ)

(-) Sites  (0, 0)

(no "Site" information available for 1OUZ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_LIKEPS00045 Bacterial histone-like DNA-binding proteins signature.IHFB_ECOLI47-66  1B:47-66
IHFA_ECOLI48-67  1A:48-67

(-) Exons   (0, 0)

(no "Exon" information available for 1OUZ)

(-) 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:96
 aligned with IHFA_ECOLI | P0A6X7 from UniProtKB/Swiss-Prot  Length:99

    Alignment length:96
                                    11        21        31        41        51        61        71        81        91      
            IHFA_ECOLI    2 ALTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENASPK 97
               SCOP domains d1ouza_ A: Integration host factor alpha subunit (IHFA)                                          SCOP domains
               CATH domains 1ouzA00 A:2-97 HU Protein, subunit A                                                             CATH domains
               Pfam domains -Bac_DNA_binding-1ouzA01 A:3-92                                                            ----- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...eee...eeeeeeee..eeee......eeee..eeeeeeeehhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ----------------------------------------------HISTONE_LIKE        ------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                  1ouz A  2 ALTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENASPK 97
                                    11        21        31        41        51        61        71        81        91      


Chain B from PDB  Type:PROTEIN  Length:94
 aligned with IHFB_ECOLI | P0A6Y1 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:94
                                    10        20        30        40        50        60        70        80        90    
            IHFB_ECOLI    1 MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHFKPGKELRDRANIYG 94
               SCOP domains d1ouzb_ B: Integration host factor beta subunit (IHFB)                                         SCOP domains
               CATH domains 1ouzB00 B:1-94 HU Protein, subunit A                                                           CATH domains
               Pfam domains Bac_DNA_binding-1ouzB01 B:1-91                                                             --- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...eee...eeeeeeee..eeee......eeee..eeeeeeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------HISTONE_LIKE        ---------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  1ouz B  1 MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIAIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHFKPGKELRDRANIYG 94
                                    10        20        30        40        50        60        70        80        90    


Chain C from PDB  Type:DNA  Length:35
                                                                  
                  1ouz C 50 CGGTGCTACAAATTGATAAGCAATGCTTTTTTGGC 16
                            ||||||||41||||||||31||||||||21|||||
                           50|||||||41|||||||32|||||||23|||||||
                            49|||||||40|||||||31|||||||22||||||
                             48|||||| 39|||||| 30|||||| 21|||||
                              47|||||  38|||||  29|||||  20||||
                               46||||   37||||   28||||   19|||
                                45|||    36|||    27|||    18||
                                 44||     35||     26||     17|
                                  43|      34|      25|      16
                                   42       33       24        


Chain D from PDB  Type:DNA  Length:15
                                              
                  1ouz D 15 GGCCAAAAAAGCATT 29
                                    24     


Chain E from PDB  Type:DNA  Length:20
                                                   
                  1ouz E 30 GCTTATCAATTTGTAGCACC 49
                                    39        49
   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, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Bac_DNA_binding] (8)

(-) Gene Ontology  (12, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IHFA_ECOLI | P0A6X7)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0000746    conjugation    The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.
    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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases 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:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain B   (IHFB_ECOLI | P0A6Y1)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0000746    conjugation    The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.
    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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases 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:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IHFA_ECOLI | P0A6X7: 1ihf 1owf 1owg 2ht0 2iie 2iif 5j0n
        IHFB_ECOLI | P0A6Y1: 1ihf 1owf 1owg 2ht0 2iie 2iif 5j0n

(-) Related Entries Specified in the PDB File

1ihf CRYSTAL STRUCTURE OF AN IHF-DNA COMPLEX: A PROTEIN-INDUCED DNA U-TURN