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(-) Description

Title :  STRUCTURE OF FITAB BOUND TO IR36 DNA FRAGMENT
 
Authors :  K. Mattison, J. S. Wilbur, M. So, R. G. Brennan
Date :  16 May 06  (Deposition) - 26 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,U,V
Keywords :  Pin Domain, Rhh Protein, Dna Binding, Tetramer Of Dimers, Gene Regulation/Dna Complex Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Mattison, J. S. Wilbur, M. So, R. G. Brennan
Structure Of Fitab From Neisseria Gonorrhoeae Bound To Dna Reveals A Tetramer Of Toxin-Antitoxin Heterodimers Containing Pin Domains And Ribbon-Helix-Helix Motifs.
J. Biol. Chem. V. 281 37942 2006
PubMed-ID: 16982615  |  Reference-DOI: 10.1074/JBC.M605198200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IR36-STRAND 1
    Chains: U
    Engineered: YES
    Mutation: YES
    Other Details: SEQUENCE UPSTREAM OF FITAB PROMOTER REGION
    Synthetic: YES
 
Molecule 2 - IR36-STRAND 2
    Chains: V
    Engineered: YES
    Mutation: YES
    Other Details: SEQUENCE UPSTREAM OF FITAB PROMOTER REGION
    Synthetic: YES
 
Molecule 3 - TRAFFICKING PROTEIN B
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PET
    Gene: FITB
    Organism Scientific: NEISSERIA GONORRHOEAE
    Organism Taxid: 485
 
Molecule 4 - TRAFFICKING PROTEIN A
    Chains: E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PET
    Gene: FITA
    Organism Scientific: NEISSERIA GONORRHOEAE
    Organism Taxid: 485

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit : ABCDEFGHUV

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
15IU2Mod. Nucleotide5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 2H1O)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2H1O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2H1O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H1O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2H1O)

(-) Exons   (0, 0)

(no "Exon" information available for 2H1O)

(-) 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:143
 aligned with FITB_NEIG1 | Q5F882 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:143
                                                                                                                                                                    139    
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        |-   
           FITB_NEIG1     1 MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAELRLGVALLLNGKKKNVLHERLEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSLTVATRDTGSFFAADVAVFNPWHD----   -
               SCOP domains d2h1oa1 A:1-138 Trafficking protein B                                                                                                     ----- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhh...hhhhhhhhhh.hhh.eeeehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..ee..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..eee..hhhhhhhhh..ee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h1o A   1 MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAEMRLGVALLLNGKKKNVLHERMEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSMTVATRDTGSFFAADVAVFNPWHLEHHH 143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   


Chain B from PDB  Type:PROTEIN  Length:140
 aligned with FITB_NEIG1 | Q5F882 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:140
                                                                                                                                                                    139 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        |-
           FITB_NEIG1     1 MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAELRLGVALLLNGKKKNVLHERLEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSLTVATRDTGSFFAADVAVFNPWHD-   -
               SCOP domains d2h1ob1 B:1-138 Trafficking protein B                                                                                                     -- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhh.......hhhhhhhhhhhhhh.eeeehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..ee..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..eee..hhhhhhhh...ee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h1o B   1 MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAEMRLGVALLLNGKKKNVLHERMEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSMTVATRDTGSFFAADVAVFNPWHLE 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140


Chain C from PDB  Type:PROTEIN  Length:143
 aligned with FITB_NEIG1 | Q5F882 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:143
                                                                                                                                                                    139    
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        |-   
           FITB_NEIG1     1 MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAELRLGVALLLNGKKKNVLHERLEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSLTVATRDTGSFFAADVAVFNPWHD----   -
               SCOP domains d2h1oc1 C:1-138 Trafficking protein B                                                                                                     ----- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhh...hhhhhhhhhhhhhh.eeeehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..ee..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..eee..hhhhhhhhh..ee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h1o C   1 MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAEMRLGVALLLNGKKKNVLHERMEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSMTVATRDTGSFFAADVAVFNPWHLEHHH 143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   


Chain D from PDB  Type:PROTEIN  Length:140
 aligned with FITB_NEIG1 | Q5F882 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:140
                                                                                                                                                                    139 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        |-
           FITB_NEIG1     1 MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAELRLGVALLLNGKKKNVLHERLEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSLTVATRDTGSFFAADVAVFNPWHD-   -
               SCOP domains d2h1od1 D:1-138 Trafficking protein B                                                                                                     -- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhh...hhhhhhhhhhhhhh.eeeehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.eee..hhhhhhhh...ee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h1o D   1 MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAEMRLGVALLLNGKKKNVLHERMEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSMTVATRDTGSFFAADVAVFNPWHLE 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140


Chain E from PDB  Type:PROTEIN  Length:68
 aligned with FITA_NEIG1 | Q5F881 from UniProtKB/Swiss-Prot  Length:78

    Alignment length:68
                                    11        21        31        41        51        61        
           FITA_NEIG1     2 ASVVIRNLSEATHNAIKFRARAAGRSTEAEIRLILDNIAKAQQTVRLGSMLASIGQEIGGVELEDVRG  69
               SCOP domains d2h1oe1 E:2-69 Trafficking protein A                                 SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 2h1o E   2 ASVVIRNLSEATHNAIKFRARAAGRSTEAEIRLILDNIAKAQQTVRLGSMLASIGQEIGGVELEDVRG  69
                                    11        21        31        41        51        61        


Chain F from PDB  Type:PROTEIN  Length:64
 aligned with FITA_NEIG1 | Q5F881 from UniProtKB/Swiss-Prot  Length:78

    Alignment length:64
                                    11        21        31        41        51        61    
           FITA_NEIG1     2 ASVVIRNLSEATHNAIKFRARAAGRSTEAEIRLILDNIAKAQQTVRLGSMLASIGQEIGGVELE  65
               SCOP domains d2h1of1 F:2-65 Trafficking protein A                             SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 2h1o F   2 ASVVIRNLSEATHNAIKFRARAAGRSTEAEIRLILDNIAKAQQTVRLGSMLASIGQEIGGVELE  65
                                    11        21        31        41        51        61    


Chain G from PDB  Type:PROTEIN  Length:67
 aligned with FITA_NEIG1 | Q5F881 from UniProtKB/Swiss-Prot  Length:78

    Alignment length:67
                                    11        21        31        41        51        61       
           FITA_NEIG1     2 ASVVIRNLSEATHNAIKFRARAAGRSTEAEIRLILDNIAKAQQTVRLGSMLASIGQEIGGVELEDVR  68
               SCOP domains d2h1og1 G:2-68 Trafficking protein A                                SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 2h1o G   2 ASVVIRNLSEATHNAIKFRARAAGRSTEAEIRLILDNIAKAQQTVRLGSMLASIGQEIGGVELEDVR  68
                                    11        21        31        41        51        61       


Chain H from PDB  Type:PROTEIN  Length:63
 aligned with FITA_NEIG1 | Q5F881 from UniProtKB/Swiss-Prot  Length:78

    Alignment length:63
                                    11        21        31        41        51        61   
           FITA_NEIG1     2 ASVVIRNLSEATHNAIKFRARAAGRSTEAEIRLILDNIAKAQQTVRLGSMLASIGQEIGGVEL  64
               SCOP domains d2h1oh1 H:2-64 Trafficking protein A                            SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 2h1o H   2 ASVVIRNLSEATHNAIKFRARAAGRSTEAEIRLILDNIAKAQQTVRLGSMLASIGQEIGGVEL  64
                                    11        21        31        41        51        61   


Chain U from PDB  Type:DNA  Length:36
                                                                    
                 2h1o U   1 AGATTGCTATCATTTTTTTTATTTTGATAGCATuTG  36
                                    10        20        30   |  
                                                            34-5IU


Chain V from PDB  Type:DNA  Length:36
                                                                    
                 2h1o V  37 CAAATGCTATCAAAAuAAAAAAAATGATAGCAATCT  72
                                    46     |  56        66      
                                          52-5IU
   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, 8)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2H1O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H1O)

(-) Gene Ontology  (13, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (FITB_NEIG1 | Q5F882)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0044001    migration in host    The directional movement of an organism from one place to another within its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

Chain E,F,G,H   (FITA_NEIG1 | Q5F881)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0044001    migration in host    The directional movement of an organism from one place to another within its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

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  2h1o
    Family and Domain Information: ProDom | SYSTERS
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  FITA_NEIG1 | Q5F881
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  FITB_NEIG1 | Q5F882
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 Related Entries

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

UniProtKB/Swiss-Prot
        FITA_NEIG1 | Q5F881: 2bsq 2h1c
        FITB_NEIG1 | Q5F882: 2bsq 2h1c

(-) Related Entries Specified in the PDB File

2h1c FRAGMENT OF PROTEIN PROTEIN OF STRUCTURE