2VII - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   PSPF1-275-MG-AMP

Authors :   N. Joly, M. Rappas, M. Buck, X. Zhang

Date :   04 Dec 07 (Deposition) - 22 Jan 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

Chains :   Asym./Biol. Unit : A

Keywords :   Aaa, Pspf, Activator, Atp-Binding, Dna-Binding, Sigma54 Activator, Nucleotide-Binding, Transcription, Gene Regulation, Enhancer Binding Protein, Transcription Activation, Transcription Regulation, Two-Component Regulatory System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Joly, M. Rappas, M. Buck, X. Zhang
Trapping Of A Transcription Complex Using A New Nucleotide Analogue: Amp Aluminium Fluoride
J. Mol. Biol. V. 375 1206 2008
PubMed-ID: 18082766 | Reference-DOI: 10.1016/J.JMB.2007.11.050

Molecule 1 - PSP OPERON TRANSCRIPTIONAL ACTIVATOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	B834
	Expression System Taxid	:	562
	Expression System Vector	:	PET28B
	Fragment	:	AAA DOMAIN, RESIDUES 1-259
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Other Details	:	ADENOSINE MONOPHOSPHATE (AMP)
	Strain	:	K12

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:7 , LEU A:8 , LEU A:9 , GLY A:39 , THR A:40 , GLY A:41 , LYS A:42 , GLU A:43 , LEU A:44 , GLU A:125 , MET A:189 , ILE A:226 , ARG A:227 , MG A:261 , HOH A:2057 , HOH A:2107	BINDING SITE FOR RESIDUE AMP A 260
2	AC2	SOFTWARE	GLU A:43 , AMP A:260	BINDING SITE FOR RESIDUE MG A 261

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

Asymmetric/Biological Unit

No.	Residues
1	Arg A:258	-	Pro A:259

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

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIGMA54_INTERACT_4	PS50045	Sigma-54 interaction domain profile.	PSPF_ECOLI	8-238	1	A:8-238
2	SIGMA54_INTERACT_2	PS00676	Sigma-54 interaction domain ATP-binding region B signature.	PSPF_ECOLI	94-109	1	A:94-109
3	SIGMA54_INTERACT_3	PS00688	Sigma-54 interaction domain C-terminal part signature.	PSPF_ECOLI	222-231	1	A:222-231

(no "Exon" information available for 2VII)

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:247
 aligned with PSPF_ECOLI | P37344 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:253
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256   
           PSPF_ECOLI     7 NLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNENLLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATAPMMVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRADLLDRLAFDVVQLPPLRERESDIMLMAEYFAIQMCREIKLPLFPGFTERARETLLNYRWPGNIRELKNVVERSVYRHGTSDYPLDDIIIDPFKRRP 259
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2viiA01 A:7-179 P-loop containing nucleotide triphosphate hydrolases                                                                                                         2viiA02 A:180-259  [code=1.10.8.60, no name defined]                             CATH domains
               Pfam domains -Sigma54_activat-2viiA01 A:8-175                                                                                                                                         ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhh...------.....hhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhee........ee..eeeeeee..hhhhhhhh...hhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -SIGMA54_INTERACT_4  PDB: A:8-238 UniProt: 8-238                                                                                                                                                                                        --------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------SIGMA54_INTERACT----------------------------------------------------------------------------------------------------------------SIGMA54_IN---------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vii A   7 NLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNENLLDSELFGHEA------QKRHPGRFERADGGTLFLDELATAPMMVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRADLLDRLAFDVVQLPPLRERESDIMLMAEYFAIQMCREIKLPLFPGFTERARETLLNYRWPGNIRELKNVVERSVYRHGTSDYPLDDIIIDPFKRRP 259
                                    16        26        36        46        56        66        76     |   -  |     96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256   
                                                                                                      82     89

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 2VII)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Sigma54_activat (5)

Escherichia coli (strain K12) (1)

Sigma54_activat-2viiA01

A:8-175

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PSPF_ECOLI | P37344)

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:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	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:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		AMP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Arg A:258 - Pro A:259	[ RasMol ]

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	2vii
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
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Access by UniProt ID/Accession number
	PSPF_ECOLI \| P37344
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
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		Disease Information	:	OMIM

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		Age Related Information	:	GenAge

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
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	PSPF_ECOLI \| P37344
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UniProtKB/Swiss-Prot
	PSPF_ECOLI \| P37344	:	2bjv 2bjw 2c96 2c98 2c99 2c9c 4qnm 4qnr 4qos 5nss

2bjv	CRYSTAL STRUCTURE OF PSPF(1-275) R168A MUTANT
2bjw	PSPF AAA DOMAIN
2c96	STRUCTURAL BASIS OF THE NUCLEOTIDE DRIVEN CONFORMATIONAL CHANGES IN THE AAA DOMAIN OF TRANSCRIPTION ACTIVATOR PSPF
2c98	STRUCTURAL BASIS OF THE NUCLEOTIDE DRIVEN CONFORMATIONAL CHANGES IN THE AAA DOMAIN OF TRANSCRIPTION ACTIVATOR PSPF
2c99	STRUCTURAL BASIS OF THE NUCLEOTIDE DRIVEN CONFORMATIONAL CHANGES IN THE AAA DOMAIN OF TRANSCRIPTION ACTIVATOR PSPF
2c9c	STRUCTURAL BASIS OF THE NUCLEOTIDE DRIVEN CONFORMATIONAL CHANGES IN THE AAA DOMAIN OF TRANSCRIPTION ACTIVATOR PSPF

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (2, 2)

Pfam Domains (1, 1)

Gene Ontology (11, 11)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File