3QOQ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE TRANSCRIPTION FACTOR AMRZ IN COMPLEX WITH THE 18 BASE PAIR AMRZ1 BINDING SITE

Authors :   E. E. Pryor Jr. , D. J. Wozniak, T. Hollis

Date :   10 Feb 11 (Deposition) - 15 Feb 12 (Release) - 17 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Protein-Dna Complex, Ribbon-Helix-Helix, Transcription Factor, Dna Binding, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. E. Pryor Jr. , E. A. Waligora, B. Xu, S. Dellos-Nolan, D. J. Wozniak, T. Hollis
The Transcription Factor Amrz Utilizes Multiple Dna Binding Modes To Recognize Activator And Repressor Sequences Of Pseudomonas Aeruginosa Virulence Genes.
Plos Pathog. V. 8 02648 2012
PubMed-ID: 22511872 | Reference-DOI: 10.1371/JOURNAL.PPAT.1002648

Molecule 1 - ALGINATE AND MOTILITY REGULATOR Z
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET19
	Expression System Strain	:	C41(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1-66
	Gene	:	ALGZ, AMRZ, PA3385
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Strain	:	PA01
	Synonym	:	DNA BINDING-PROTEIN

*Molecule 2 - DNA (5'- D(APCPTPGPGPCPAPAPAPAPCPGPCPCPGPGPCPA)-3')*
	Chains	:	E
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 3 - DNA (5'- D(TPGPCPCPGPGPCPGPTPTPTPTPGPCPCPAPGPT)-3')*
	Chains	:	F
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3QOQ)

(no "SS Bond" information available for 3QOQ)

(no "Cis Peptide Bond" information available for 3QOQ)

(no "SAP(SNP)/Variant" information available for 3QOQ)

(no "PROSITE Motif" information available for 3QOQ)

(no "Exon" information available for 3QOQ)

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:50
 aligned with G3XCY4_PSEAE | G3XCY4 from UniProtKB/TrEMBL  Length:108

    Alignment length:50
                                    19        29        39        49        59
          G3XCY4_PSEAE   10 TYSSRTADKFVVRLPEGMREQIAEVARSHHRSMNSEIIARLEQSLLQEGA 59
               SCOP domains -------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  3qoq A 10 TYSSRTADKFVVRLPEGmREQIAEVARSHHRSmNSEIIARLEQSLLQEGA 59
                                    19       |29        39  |     49        59
                                            27-MSE         42-MSE

Chain A from PDB  Type:PROTEIN  Length:50
 aligned with Q9RPY7_PSEAI | Q9RPY7 from UniProtKB/TrEMBL  Length:108

    Alignment length:50
                                    19        29        39        49        59
          Q9RPY7_PSEAI   10 TYSSRTADKFVVRLPEGMREQIAEVARSHHRSMNSEIIARLEQSLLQEGA 59
               SCOP domains -------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  3qoq A 10 TYSSRTADKFVVRLPEGmREQIAEVARSHHRSmNSEIIARLEQSLLQEGA 59
                                    19       |29        39  |     49        59
                                            27-MSE         42-MSE

Chain B from PDB  Type:PROTEIN  Length:44
 aligned with G3XCY4_PSEAE | G3XCY4 from UniProtKB/TrEMBL  Length:108

    Alignment length:44
                                    25        35        45        55    
          G3XCY4_PSEAE   16 ADKFVVRLPEGMREQIAEVARSHHRSMNSEIIARLEQSLLQEGA 59
               SCOP domains -------------------------------------------- SCOP domains
               CATH domains -------------------------------------------- CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                  3qoq B 16 ADKFVVRLPEGmREQIAEVARSHHRSmNSEIIARLEQSLLQEGA 59
                                    25 |      35      | 45        55    
                                      27-MSE         42-MSE

Chain B from PDB  Type:PROTEIN  Length:44
 aligned with Q9RPY7_PSEAI | Q9RPY7 from UniProtKB/TrEMBL  Length:108

    Alignment length:44
                                    25        35        45        55    
          Q9RPY7_PSEAI   16 ADKFVVRLPEGMREQIAEVARSHHRSMNSEIIARLEQSLLQEGA 59
               SCOP domains -------------------------------------------- SCOP domains
               CATH domains -------------------------------------------- CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                  3qoq B 16 ADKFVVRLPEGmREQIAEVARSHHRSmNSEIIARLEQSLLQEGA 59
                                    25 |      35      | 45        55    
                                      27-MSE         42-MSE

Chain C from PDB  Type:PROTEIN  Length:49
 aligned with G3XCY4_PSEAE | G3XCY4 from UniProtKB/TrEMBL  Length:108

    Alignment length:49
                                    19        29        39        49         
          G3XCY4_PSEAE   10 TYSSRTADKFVVRLPEGMREQIAEVARSHHRSMNSEIIARLEQSLLQEG 58
               SCOP domains ------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeee..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------- Transcript
                  3qoq C 10 TYSSRTADKFVVRLPEGmREQIAEVARSHHRSmNSEIIARLEQSLLQEG 58
                                    19       |29        39  |     49         
                                            27-MSE         42-MSE

Chain C from PDB  Type:PROTEIN  Length:49
 aligned with Q9RPY7_PSEAI | Q9RPY7 from UniProtKB/TrEMBL  Length:108

    Alignment length:49
                                    19        29        39        49         
          Q9RPY7_PSEAI   10 TYSSRTADKFVVRLPEGMREQIAEVARSHHRSMNSEIIARLEQSLLQEG 58
               SCOP domains ------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeee..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------- Transcript
                  3qoq C 10 TYSSRTADKFVVRLPEGmREQIAEVARSHHRSmNSEIIARLEQSLLQEG 58
                                    19       |29        39  |     49         
                                            27-MSE         42-MSE

Chain D from PDB  Type:PROTEIN  Length:48
 aligned with G3XCY4_PSEAE | G3XCY4 from UniProtKB/TrEMBL  Length:108

    Alignment length:48
                                    25        35        45        55        
          G3XCY4_PSEAE   16 ADKFVVRLPEGMREQIAEVARSHHRSMNSEIIARLEQSLLQEGALQDN 63
               SCOP domains ------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                  3qoq D 16 ADKFVVRLPEGmREQIAEVARSHHRSmNSEIIARLEQSLLQEGALQDN 63
                                    25 |      35      | 45        55        
                                      27-MSE         42-MSE

Chain D from PDB  Type:PROTEIN  Length:48
 aligned with Q9RPY7_PSEAI | Q9RPY7 from UniProtKB/TrEMBL  Length:108

    Alignment length:48
                                    25        35        45        55        
          Q9RPY7_PSEAI   16 ADKFVVRLPEGMREQIAEVARSHHRSMNSEIIARLEQSLLQEGALQDN 63
               SCOP domains ------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                  3qoq D 16 ADKFVVRLPEGmREQIAEVARSHHRSmNSEIIARLEQSLLQEGALQDN 63
                                    25 |      35      | 45        55        
                                      27-MSE         42-MSE

Chain E from PDB  Type:DNA  Length:18
                                                 
                  3qoq E  1 ACTGGCAAAACGCCGGCA 18
                                    10

Chain F from PDB  Type:DNA  Length:18
                                                 
                  3qoq F 19 TGCCGGCGTTTTGCCAGT 36
                                    28

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 '\|'

(no "SCOP Domain" information available for 3QOQ)

(no "CATH Domain" information available for 3QOQ)

(no "Pfam Domain" information available for 3QOQ)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (G3XCY4_PSEAE | G3XCY4)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0044212	transcription regulatory region DNA binding	Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:2000147	positive regulation of cell motility	Any process that activates or increases the frequency, rate or extent of cell motility.
	GO:1900233	positive regulation of single-species biofilm formation on inanimate substrate	Any process that activates or increases the frequency, rate or extent of single-species biofilm formation on inanimate substrate.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

Chain A,B,C,D (Q9RPY7_PSEAI | Q9RPY7)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0044212	transcription regulatory region DNA binding	Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
biological process
	GO:2000147	positive regulation of cell motility	Any process that activates or increases the frequency, rate or extent of cell motility.
	GO:1900233	positive regulation of single-species biofilm formation on inanimate substrate	Any process that activates or increases the frequency, rate or extent of single-species biofilm formation on inanimate substrate.
	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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(no "Sites" information available for 3qoq)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3qoq)

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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