4A0X - JenaLib

Title :   STRUCTURE OF THE GLOBAL TRANSCRIPTION REGULATOR FAPR FROM STAPHYLOCOCCUS AUREUS

Authors :   D. Albanesi, M. E. Guerin, A. Buschiazzo, D. De Mendoza, P. M. Alzari

Date :   13 Sep 11 (Deposition) - 26 Sep 12 (Release) - 23 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A
Biol. Unit 1: A  (6x)

Keywords :   Transcription, Lipid Homeostasis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Albanesi, G. Reh, M. E. Guerin, F. Schaeffer, M. Debarbouille, A. Buschiazzo, G. E. Schujman, D. De Mendoza, P. M. Alzari
Structural Basis For Feed-Forward Transcriptional Regulation Of Membrane Lipid Homeostasis In Staphylococcus Aureus.
Plos Pathog. V. 9 3108 2013
PubMed-ID: 23300457 | Reference-DOI: 10.1371/JOURNAL.PPAT.1003108

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:64 , GLU A:74 , GLU A:75 , HIS A:104	BINDING SITE FOR RESIDUE ZN A 201
2	AC2	SOFTWARE	HIS A:112 , ACT A:211	BINDING SITE FOR RESIDUE ZN A 202
3	AC3	SOFTWARE	HIS A:134 , HIS A:163 , HOH A:2016 , HOH A:2020	BINDING SITE FOR RESIDUE ZN A 203
4	AC4	SOFTWARE	GLU A:31 , HIS A:174 , HOH A:2004	BINDING SITE FOR RESIDUE ZN A 204
5	AC5	SOFTWARE	HIS A:30 , ASP A:34 , HOH A:2002 , HOH A:2003	BINDING SITE FOR RESIDUE ZN A 205
6	AC6	SOFTWARE	HIS A:112 , VAL A:113 , ZN A:202	BINDING SITE FOR RESIDUE ACT A 211
7	AC7	SOFTWARE	PHE A:103 , ARG A:110 , GLY A:111 , HIS A:112 , ASN A:119	BINDING SITE FOR RESIDUE ACT A 212
8	AC8	SOFTWARE	TYR A:67 , GLU A:75 , PHE A:78 , ILE A:79 , GLY A:80	BINDING SITE FOR RESIDUE MES A 221

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:184
 aligned with Q2FZ56_STAA8 | Q2FZ56 from UniProtKB/TrEMBL  Length:190

    Alignment length:184
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185    
         Q2FZ56_STAA8     6 LKLKKDKRREAIRQQIDSNPFITDHELSDLFQVSIQTIRLDRTYLNIPELRKRIKLVAEKNYDQISSIEEQEFIGDLIQVNPNVKAQSILDITSDSVFHKTGIARGHVLFAQANSLCVALIKQPTVLTHESSIQFIEKVKLNDTVRAEARVVNQTAKHYYVEVKSYVKHTLVFKGNFKMFYDKR 189
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhh..eeeeee...eeeeeee.hhhh........hhhhhhhhhhhhhhhhh...eeeeeeeeeee........eeeeeeeeeee...eeeeeeeeee..eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a0x A   6 LKLKKDKRREAIRQQIDSNPFITDHELSDLFQVSIQTIRLDRTYLNIPELRKRIKLVAEKNYDQISSIEEQEFIGDLIQVNPNVKAQSILDITSDSVFHKTGIARGHVLFAQANSLCVALIKQPTVLTHESSIQFIEKVKLNDTVRAEARVVNQTAKHYYVEVKSYVKHTLVFKGNFKMFYDKR 189
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A (Q2FZ56_STAA8 | Q2FZ56)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0006633	fatty acid biosynthetic process	The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
	GO:0006631	fatty acid metabolic process	The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0045717	negative regulation of fatty acid biosynthetic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids.
	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: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.

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MES	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4a0x)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	4a0x
		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
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	Q2FZ56_STAA8 \| Q2FZ56
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	Q2FZ56_STAA8 \| Q2FZ56
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description