1ZG5 | PD0646 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   NARL COMPLEXED TO NARG-89 PROMOTER PALINDROMIC TAIL-TO-TAIL DNA SITE

Authors :   A. E. Maris, M. Kaczor-Grzeskowiak, Z. Ma, M. L. Kopka, R. P. Gunsalus, R. E. Dickerson

Date :   20 Apr 05 (Deposition) - 22 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: E,F,G,H  (1x)

Keywords :   Protein-Dna Complex, Helix-Turn-Helix, Two-Component Response Regulator, Dna Bending, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. E. Maris, M. Kaczor-Grzeskowiak, Z. Ma, M. L. Kopka, R. P. Gunsalus, R. E. Dickerson
Primary And Secondary Modes Of Dna Recognition By The Narl Two-Component Response Regulator.
Biochemistry V. 44 14538 2005
PubMed-ID: 16262254 | Reference-DOI: 10.1021/BI050734U
(for further references see the PDB file header)

*Molecule 1 - 5'- D(CPGPTPAPCPCPCPCPTPAPTPAPGPGPGPGPTPAPCP G)-3'*
	Chains	:	C, D, G, H
	Engineered	:	YES
	Other Details	:	SOLID PHASE SYNTHESIS
	Synthetic	:	YES

Molecule 2 - NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL
	Chains	:	A, B, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMJ05
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	DNA BINDING DOMAIN (RESIDUES 147-216)
	Gene	:	NARL
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:					E	F	G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 24)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	12	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 12)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG F:161 , HOH F:342	BINDING SITE FOR RESIDUE SO4 F 301
02	AC2	SOFTWARE	ARG A:161	BINDING SITE FOR RESIDUE SO4 A 302
03	AC3	SOFTWARE	PRO B:158 , ARG B:161 , HOH B:329	BINDING SITE FOR RESIDUE SO4 B 303
04	AC4	SOFTWARE	SER F:185 , LYS F:188 , HOH F:325 , HOH F:326 , DC G:5 , DC G:6 , HOH H:50 , HOH H:52	BINDING SITE FOR RESIDUE SO4 F 304
05	AC5	SOFTWARE	SER A:185 , LYS A:188 , HOH A:312 , HOH C:27 , HOH C:52 , DC D:25 , DC D:26	BINDING SITE FOR RESIDUE SO4 A 305
06	AC6	SOFTWARE	SER B:185 , LYS B:188 , HOH B:325 , HOH B:334 , HOH B:341 , DC C:6 , HOH D:53 , HOH D:63	BINDING SITE FOR RESIDUE SO4 B 306
07	AC7	SOFTWARE	SER E:185 , LYS E:188 , HOH E:323 , HOH E:324 , HOH G:30 , HOH G:51 , DC H:25 , DC H:26	BINDING SITE FOR RESIDUE SO4 E 307
08	AC8	SOFTWARE	PRO E:158 , ARG E:161	BINDING SITE FOR RESIDUE SO4 E 308
09	AC9	SOFTWARE	ARG A:178	BINDING SITE FOR RESIDUE SO4 A 309
10	BC1	SOFTWARE	ARG B:178	BINDING SITE FOR RESIDUE SO4 B 310
11	BC2	SOFTWARE	ARG E:178	BINDING SITE FOR RESIDUE SO4 E 311
12	BC3	SOFTWARE	ARG F:178	BINDING SITE FOR RESIDUE SO4 F 312

(no "SS Bond" information available for 1ZG5)

(no "Cis Peptide Bond" information available for 1ZG5)

(no "SAP(SNP)/Variant" information available for 1ZG5)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LUXR_1	PS00622	LuxR-type HTH domain signature.	NARL_ECOLI	170-197	4	A:170-197 B:170-197 E:170-197 F:170-197

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LUXR_1	PS00622	LuxR-type HTH domain signature.	NARL_ECOLI	170-197	2	A:170-197 B:170-197 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LUXR_1	PS00622	LuxR-type HTH domain signature.	NARL_ECOLI	170-197	2	- - E:170-197 F:170-197

(no "Exon" information available for 1ZG5)

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:66
 aligned with NARL_ECOLI | P0AF28 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:66
                                   160       170       180       190       200       210      
           NARL_ECOLI   151 RDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQERIF 216
               SCOP domains d1zg5a1 A:151-216 Nitrate/nitrite response regulator (NarL)        SCOP domains
               CATH domains 1zg5A00 A:151-216 'winged helix' repressor DNA binding domain      CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------HTH_LUXR_1  PDB: A:170-197  ------------------- PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 1zg5 A 151 RDVNQLTPRERDILKLIAQGLPNKmIARRLDITESTVKVHVKHmLKKmKLKSRVEAAVWVHQERIF 216
                                   160       170    |  180       190   |   200       210      
                                                  175-MSE            194-MSE                  
                                                                         198-MSE

Chain B from PDB  Type:PROTEIN  Length:66
 aligned with NARL_ECOLI | P0AF28 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:66
                                   160       170       180       190       200       210      
           NARL_ECOLI   151 RDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQERIF 216
               SCOP domains d1zg5b1 B:151-216 Nitrate/nitrite response regulator (NarL)        SCOP domains
               CATH domains 1zg5B00 B:151-216 'winged helix' repressor DNA binding domain      CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------HTH_LUXR_1  PDB: B:170-197  ------------------- PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 1zg5 B 151 RDVNQLTPRERDILKLIAQGLPNKmIARRLDITESTVKVHVKHmLKKmKLKSRVEAAVWVHQERIF 216
                                   160       170    |  180       190   |   200       210      
                                                  175-MSE            194-MSE                  
                                                                         198-MSE

Chain C from PDB  Type:DNA  Length:20
                                                    
                 1zg5 C   1 CGTACCCCTATAGGGGTACG  20
                                    10        20

Chain D from PDB  Type:DNA  Length:20
                                                    
                 1zg5 D  21 CGTACCCCTATAGGGGTACG  40
                                    30        40

Chain E from PDB  Type:PROTEIN  Length:67
 aligned with NARL_ECOLI | P0AF28 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:67
                                   159       169       179       189       199       209       
           NARL_ECOLI   150 ERDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQERIF 216
               SCOP domains -d1zg5e1 E:151-216 Nitrate/nitrite response regulator (NarL)        SCOP domains
               CATH domains 1zg5E00 E:150-216 'winged helix' repressor DNA binding domain       CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------HTH_LUXR_1  PDB: E:170-197  ------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 1zg5 E 150 ERDVNQLTPRERDILKLIAQGLPNKmIARRLDITESTVKVHVKHmLKKmKLKSRVEAAVWVHQERIF 216
                                   159       169     | 179       189    |  199       209       
                                                   175-MSE            194-MSE                  
                                                                          198-MSE

Chain F from PDB  Type:PROTEIN  Length:66
 aligned with NARL_ECOLI | P0AF28 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:66
                                   160       170       180       190       200       210      
           NARL_ECOLI   151 RDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQERIF 216
               SCOP domains d1zg5f1 F:151-216 Nitrate/nitrite response regulator (NarL)        SCOP domains
               CATH domains 1zg5F00 F:151-216 'winged helix' repressor DNA binding domain      CATH domains
           Pfam domains (1) --GerE-1zg5F01 F:153-210                                    ------ Pfam domains (1)
           Pfam domains (2) --GerE-1zg5F02 F:153-210                                    ------ Pfam domains (2)
           Pfam domains (3) --GerE-1zg5F03 F:153-210                                    ------ Pfam domains (3)
           Pfam domains (4) --GerE-1zg5F04 F:153-210                                    ------ Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------HTH_LUXR_1  PDB: F:170-197  ------------------- PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 1zg5 F 151 RDVNQLTPRERDILKLIAQGLPNKmIARRLDITESTVKVHVKHmLKKmKLKSRVEAAVWVHQERIF 216
                                   160       170    |  180       190   |   200       210      
                                                  175-MSE            194-MSE                  
                                                                         198-MSE

Chain G from PDB  Type:DNA  Length:20
                                                    
                 1zg5 G   1 CGTACCCCTATAGGGGTACG  20
                                    10        20

Chain H from PDB  Type:DNA  Length:20
                                                    
                 1zg5 H  21 CGTACCCCTATAGGGGTACG  40
                                    30        40

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 Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: C-terminal effector domain of the bipartite response regulators (45)

Family: GerE-like (LuxR/UhpA family of transcriptional regulators) (11)

Protein domain: Nitrate/nitrite response regulator (NarL) (5)

Escherichia coli [TaxId: 562] (5)

1a	d1zg5a1	A:151-216
1b	d1zg5f1	F:151-216
1c	d1zg5b1	B:151-216
1d	d1zg5e1	E:151-216

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

[unclassified] (77)

1a	1zg5E00	E:150-216
1b	1zg5A00	A:151-216
1c	1zg5B00	B:151-216
1d	1zg5F00	F:151-216

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: GerE (15)

Escherichia coli (strain K12) (2)

1a	GerE-1zg5F01	F:153-210
1b	GerE-1zg5F02	F:153-210
1c	GerE-1zg5F03	F:153-210
1d	GerE-1zg5F04	F:153-210

Asymmetric Unit(hide GO term definitions)

Chain A,B,E,F (NARL_ECOLI | P0AF28)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0042128	nitrate assimilation	The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances.
	GO:0000160	phosphorelay signal transduction system	A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
	GO:0010468	regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0090352	regulation of nitrate assimilation	Any process that modulates the rate, frequency, or extent of the uptake, from the environment, of nitrates, inorganic or organic salts and esters of nitric acid and the subsequent reduction of nitrate ion to other, less highly oxidized, inorganic nitrogenous substances.
	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.
cellular component
	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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1zg5)

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	1zg5
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UniProtKB/Swiss-Prot
	NARL_ECOLI \| P0AF28	:	1a04 1je8 1rnl 1zg1

1a04	FULL-LENGTH UNACTIVATED NARL
1je8	NARL COMPLEX WITH NIRB PROMOTER PALINDROMIC DNA
1rnl	FULL-LENGTH UNACTIVATED NARL
1zg1	NARL COMPLEX WITH NIRB PROMOTER NONPALINDROMIC DNA

Description

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Ligands, Modified Residues, Ions (2, 24)

Sites (12, 12)

SS Bonds (0, 0)

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