2BSQ | PD0859 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   FITAB BOUND TO DNA

Authors :   K. Mattison, J. S. Wilbur, M. So, R. G. Brennan

Date :   23 May 05 (Deposition) - 24 Aug 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,I,J

Keywords :   Transcription, Transcription Regulation Complex, Pin Domain, Ribbon-Helix-Helix, Dna Binding, Heterodimer (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

Molecule 1 - TRAFFICKING PROTEIN A
	Chains	:	E, F, G, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	DNA-BINDING PROTEIN, RESIDUES 2-78
	Organism Scientific	:	NEISSERIA GONORRHOEAE
	Organism Taxid	:	485
	Synonym	:	FITA

Molecule 2 - TRAFFICKING PROTEIN B
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	PIN DOMAIN, RESIDUES 1-139
	Mutation	:	YES
	Organism Scientific	:	NEISSERIA GONORRHOEAE
	Organism Taxid	:	485
	Synonym	:	FITB

Molecule 3 - IR36, FORWARD STRAND
	Chains	:	I
	Organism Scientific	:	NEISSERIA GONORRHOEAE
	Organism Taxid	:	485
	Synthetic	:	YES

Molecule 4 - IR36, REVERSE STRAND
	Chains	:	J
	Organism Scientific	:	NEISSERIA GONORRHOEAE
	Organism Taxid	:	485
	Synthetic	:	YES

		1	2	3	4	5	6	7	8	9	10
Asymmetric/Biological Unit	:	A	B	C	D	E	F	G	H	I	J

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	5IU	2	Mod. Nucleotide	5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE

(no "Site" information available for 2BSQ)

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

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

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

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

(no "Exon" information available for 2BSQ)

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:144
 aligned with FITB_NEIG1 | Q5F882 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:144
                                                                                                                                                                    139     
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        |-    
           FITB_NEIG1     1 MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAELRLGVALLLNGKKKNVLHERLEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSLTVATRDTGSFFAADVAVFNPWHD-----   -
               SCOP domains d2bsqa1 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
                 2bsq A   1 MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAEMRLGVALLLNGKKKNVLHERMEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSMTVATRDTGSFFAADVAVFNPWHLEHHHH 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:141
 aligned with FITB_NEIG1 | Q5F882 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:141
                                                                                                                                                                    139  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        |- 
           FITB_NEIG1     1 MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAELRLGVALLLNGKKKNVLHERLEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSLTVATRDTGSFFAADVAVFNPWHD--   -
               SCOP domains d2bsqb1 B:1-138 Trafficking protein B                                                                                                     --- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhh.......hhhhhhhhh..hhh.eeeehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..ee..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..eee..hhhhhhhh...ee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bsq B   1 MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAEMRLGVALLLNGKKKNVLHERMEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSMTVATRDTGSFFAADVAVFNPWHLEH 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain C from PDB  Type:PROTEIN  Length:144
 aligned with FITB_NEIG1 | Q5F882 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:144
                                                                                                                                                                    139     
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        |-    
           FITB_NEIG1     1 MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAELRLGVALLLNGKKKNVLHERLEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSLTVATRDTGSFFAADVAVFNPWHD-----   -
               SCOP domains d2bsqc1 C: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
                 2bsq C   1 MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAEMRLGVALLLNGKKKNVLHERMEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSMTVATRDTGSFFAADVAVFNPWHLEHHHH 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain D from PDB  Type:PROTEIN  Length:141
 aligned with FITB_NEIG1 | Q5F882 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:141
                                                                                                                                                                    139  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        |- 
           FITB_NEIG1     1 MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAELRLGVALLLNGKKKNVLHERLEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSLTVATRDTGSFFAADVAVFNPWHD--   -
               SCOP domains d2bsqd1 D:1-138 Trafficking protein B                                                                                                     --- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhh...hhhhhhhhh..hhh.eeeehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.eee..hhhhhhhh...ee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bsq D   1 MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAEMRLGVALLLNGKKKNVLHERMEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSMTVATRDTGSFFAADVAVFNPWHLEH 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain E from PDB  Type:PROTEIN  Length:69
 aligned with FITA_NEIG1 | Q5F881 from UniProtKB/Swiss-Prot  Length:78

    Alignment length:69
                                    11        21        31        41        51        61         
           FITA_NEIG1     2 ASVVIRNLSEATHNAIKFRARAAGRSTEAEIRLILDNIAKAQQTVRLGSMLASIGQEIGGVELEDVRGR  70
               SCOP domains d2bsqe1 E:2-70 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
                 2bsq E   2 ASVVIRNLSEATHNAIKFRARAAGRSTEAEIRLILDNIAKAQQTVRLGSMLASIGQEIGGVELEDVRGR  70
                                    11        21        31        41        51        61

Chain F from PDB  Type:PROTEIN  Length:65
 aligned with FITA_NEIG1 | Q5F881 from UniProtKB/Swiss-Prot  Length:78

    Alignment length:65
                                    11        21        31        41        51        61     
           FITA_NEIG1     2 ASVVIRNLSEATHNAIKFRARAAGRSTEAEIRLILDNIAKAQQTVRLGSMLASIGQEIGGVELED  66
               SCOP domains d2bsqf1 F:2-66 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
                 2bsq F   2 ASVVIRNLSEATHNAIKFRARAAGRSTEAEIRLILDNIAKAQQTVRLGSMLASIGQEIGGVELED  66
                                    11        21        31        41        51        61

Chain G 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 d2bsqg1 G:2-69 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
                 2bsq G   2 ASVVIRNLSEATHNAIKFRARAAGRSTEAEIRLILDNIAKAQQTVRLGSMLASIGQEIGGVELEDVRG  69
                                    11        21        31        41        51        61

Chain H 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 d2bsqh1 H:2-65 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
                 2bsq H   2 ASVVIRNLSEATHNAIKFRARAAGRSTEAEIRLILDNIAKAQQTVRLGSMLASIGQEIGGVELE  65
                                    11        21        31        41        51        61

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

Chain J from PDB  Type:DNA  Length:36
                                                                    
                 2bsq J  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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Ribbon-helix-helix (65)

Superfamily: Ribbon-helix-helix (65)

Family: Trafficking protein A-like (2)

Protein domain: Trafficking protein A (2)

Neisseria gonorrhoeae [TaxId: 485] (2)

1a	d2bsqe1	E:2-70
1b	d2bsqf1	F:2-66
1c	d2bsqg1	G:2-69
1d	d2bsqh1	H:2-65

Class: Alpha and beta proteins (a/b) (23833)

Fold: PIN domain-like (32)

Superfamily: PIN domain-like (32)

Family: PIN domain (11)

Protein domain: Trafficking protein B (3)

Neisseria gonorrhoeae [TaxId: 485] (3)

2a	d2bsqa1	A:1-138
2b	d2bsqb1	B:1-138
2c	d2bsqc1	C:1-138
2d	d2bsqd1	D:1-138

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

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

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.

Asymmetric/Biological Unit
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	2bsq
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	FITB_NEIG1 \| Q5F882
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UniProtKB/Swiss-Prot
	FITA_NEIG1 \| Q5F881	:	2h1c 2h1o
	FITB_NEIG1 \| Q5F882	:	2h1c 2h1o

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

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Gene Ontology (13, 16)

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