1NY5 - JenaLib

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Title :   CRYSTAL STRUCTURE OF SIGM54 ACTIVATOR (AAA+ ATPASE) IN THE INACTIVE STATE

Authors :   S. Y. Lee, A. De La Torre, S. Kustu, B. T. Nixon, D. E. Wemmer

Date :   11 Feb 03 (Deposition) - 11 Nov 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,B

Keywords :   Aaa+ Atpase, Sigma54 Activator, Bacterial Transcription, Dimer, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Y. Lee, A. De La Torre, D. Yan, S. Kustu, B. T. Nixon, D. E. Wemmer
Regulation Of The Transcriptional Activator Ntrc1: Structural Studies Of The Regulatory And Aaa+ Atpase Domain
Genes Dev. V. 17 2552 2003
PubMed-ID: 14561776 | Reference-DOI: 10.1101/GAD.1125603

Molecule 1 - TRANSCRIPTIONAL REGULATOR (NTRC FAMILY)
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	REGULATORY AND CENTRAL DOMAIN
	Gene	:	NTRC1
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 9)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	GOL	2	Ligand/Ion	GLYCEROL
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	PO4	4	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ADP A:604 , HOH A:761	BINDING SITE FOR RESIDUE MG A 500
2	AC2	SOFTWARE	HIS A:44 , ASN A:46 , ARG A:119 , LYS A:123 , GLU B:224 , GLU B:228	BINDING SITE FOR RESIDUE PO4 A 600
3	AC3	SOFTWARE	GLU A:224 , GLU A:228 , HIS B:44 , ASN B:46 , GLU B:72 , ARG B:119 , LYS B:123 , HOH B:610 , HOH B:615	BINDING SITE FOR RESIDUE PO4 B 601
4	AC4	SOFTWARE	LYS A:250 , ARG A:253 , PHE A:260 , TYR A:261 , LYS A:314 , HOH A:616 , HOH A:677 , HOH A:706 , HOH A:760	BINDING SITE FOR RESIDUE PO4 A 602
5	AC5	SOFTWARE	THR A:340 , SER A:342 , ASP A:376 , ARG A:377 , HOH A:744 , GLY B:264	BINDING SITE FOR RESIDUE PO4 A 603
6	AC6	SOFTWARE	GLU A:137 , TYR A:139 , VAL A:140 , GLY A:170 , VAL A:171 , GLY A:172 , LYS A:173 , GLU A:174 , VAL A:175 , LEU A:320 , VAL A:356 , ARG A:357 , LYS A:360 , MG A:500 , HOH A:605 , HOH A:608 , HOH A:643 , HOH A:661 , HOH A:681 , HOH A:702	BINDING SITE FOR RESIDUE ADP A 604
7	AC7	SOFTWARE	TYR B:139 , VAL B:140 , GLY B:170 , VAL B:171 , GLY B:172 , LYS B:173 , GLU B:174 , VAL B:175 , LEU B:320 , VAL B:356 , ARG B:357 , LYS B:360 , HOH B:604 , HOH B:606 , HOH B:674 , HOH B:677 , HOH B:683	BINDING SITE FOR RESIDUE ADP B 602
8	AC8	SOFTWARE	GLU B:174 , ALA B:193 , ASN B:195 , ASP B:238 , HOH B:607 , HOH B:689	BINDING SITE FOR RESIDUE GOL B 400
9	AC9	SOFTWARE	LYS A:267 , HOH A:644 , SER B:41 , ARG B:69	BINDING SITE FOR RESIDUE GOL B 401

(no "SS Bond" information available for 1NY5)

Asymmetric/Biological Unit

No.	Residues
1	Lys A:101	-	Pro A:102
2	Lys B:101	-	Pro B:102

(no "SAP(SNP)/Variant" information available for 1NY5)

(no "PROSITE Motif" information available for 1NY5)

(no "Exon" information available for 1NY5)

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:384
 aligned with O67198_AQUAE | O67198 from UniProtKB/TrEMBL  Length:439

    Alignment length:384
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380    
         O67198_AQUAE     1 MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEKHFNVVLLDLLLPDVNGLEILKWIKERSPETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHRKLRKENELLRREKDLKEEEYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIKELVKEGKFREDLYYRLGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVRELKNVIERAVLFSEGKFIDRGELSCLV 384
               SCOP domains d1ny5a1 A:1-137 Transcriptional activator sigm54 (NtrC1), N-terminal domain                                                              d1ny5a2 A:138-384 Transcriptional activator sigm54 (NtrC1), C-terminal domain                                                                                                                                                                           SCOP domains
               CATH domains 1ny5A01 A:1-136  [code=3.40.50.2300, no name defined]                                                                                   1ny5A02 A:137-311 P-loop containing nucleotide triphosphate hydrolases                                                                                                         1ny5A03 A:312-384  [code=1.10.8.60, no name defined]                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh...eeeee......hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhh......eeeee....hhhhhhhhhhh..............hhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhee........ee...eeeeee..hhhhhhhh...hhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhh...hhhhhhhhhhhhhhhhh...eehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ny5 A   1 MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEKHFNVVLLDLLLPDVNGLEILKWIKERSPETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHRKLRKENELLRREKDLKEEEYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIKELVKEGKFREDLYYRLGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVRELKNVIERAVLFSEGKFIDRGELSCLV 384
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380

Chain B from PDB  Type:PROTEIN  Length:385
 aligned with O67198_AQUAE | O67198 from UniProtKB/TrEMBL  Length:439

    Alignment length:385
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380     
         O67198_AQUAE     1 MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEKHFNVVLLDLLLPDVNGLEILKWIKERSPETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHRKLRKENELLRREKDLKEEEYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIKELVKEGKFREDLYYRLGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVRELKNVIERAVLFSEGKFIDRGELSCLVN 385
               SCOP domains d1ny5b1 B:1-137 Transcriptional activator sigm54 (NtrC1), N-terminal domain                                                              d1ny5b2 B:138-385 Transcriptional activator sigm54 (NtrC1), C-terminal domain                                                                                                                                                                            SCOP domains
               CATH domains 1ny5B01 B:1-136  [code=3.40.50.2300, no name defined]                                                                                   1ny5B02 B:137-311 P-loop containing nucleotide triphosphate hydrolases                                                                                                         1ny5B03 B:312-385  [code=1.10.8.60, no name defined]                       CATH domains
           Pfam domains (1) --Response_reg-1ny5B01 B:3-113                                                                                   -------------------------Sigma54_activat-1ny5B03 B:139-306                                                                                                                                       ------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --Response_reg-1ny5B02 B:3-113                                                                                   -------------------------Sigma54_activat-1ny5B04 B:139-306                                                                                                                                       ------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh...eeeee......hhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhh.......eeeee....hhhhhhhhhhh..............hhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhee........ee...eeeeee..hhhhhhhh...hhhhhhhhh.eeee......hhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhh...hhhhhhhhhhhhhhhh....ee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ny5 B   1 MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEKHFNVVLLDLLLPDVNGLEILKWIKERSPETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHRKLRKENELLRREKDLKEEEYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIKELVKEGKFREDLYYRLGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVRELKNVIERAVLFSEGKFIDRGELSCLVN 385
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380

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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CheY (97)

Family: Response_reg (94)

Aquifex aeolicus (4)

1a	Response_reg-1ny5B01	B:3-113
1b	Response_reg-1ny5B02	B:3-113

Clan: P-loop_NTPase (1112)

Family: Sigma54_activat (5)

Aquifex aeolicus (3)

2a	Sigma54_activat-1ny5B03	B:139-306
2b	Sigma54_activat-1ny5B04	B:139-306

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (O67198_AQUAE | O67198)

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.
	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.
	GO:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
	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: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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Asymmetric/Biological Unit
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		Lys B:101 - Pro B:102	[ RasMol ]

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	O67198_AQUAE \| O67198	:	1ny6 1zy2 3m0e 4bs1 4bt0 4bt1 4l4u 4l5e 4ly6 4lzz

(no "Related Entries Specified in the PDB File" available for 1NY5)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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