2JSX - JenaLib

Title :   SOLUTION STRUCTURE OF THE E. COLI TAT PROOFREADING CHAPERONE PROTEIN NAPD

Authors :   C. A. E. M. Spronk, G. W. Vuister, F. Sargent

Date :   17 Jul 07 (Deposition) - 21 Aug 07 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Napd, Tat, Proofreading, Protein, Nmr, Cytoplasm, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Maillard, C. A. E. M. Spronk, G. Buchanan, V. Lyall, D. J. Richardson, T. Palmer, G. W. Vuister, F. Sargent
Structural Diversity In Twin-Arginine Signal Peptide-Binding Proteins.
Proc. Natl. Acad. Sci. Usa V. 104 15641 2007
PubMed-ID: 17901208 | Reference-DOI: 10.1073/PNAS.0703967104
(for further references see the PDB file header)

Compounds

Molecule 1 - PROTEIN NAPD
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI K12
	Expression System Plasmid	:	PQE70
	Expression System Strain	:	K-12
	Expression System Taxid	:	83333
	Expression System Vector Type	:	PLASMID
	Gene	:	NAPD
	Organism Scientific	:	ESCHERICHIA COLI K12
	Organism Taxid	:	83333
	Strain	:	K-12

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

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

NMR Structure

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:95
 aligned with NAPD_ECOLI | P0A9I5 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:95
                                                                                                                 87        
                                    10        20        30        40        50        60        70        80      |  -     
            NAPD_ECOLI    1 MHTNWQVCSLVVQAKSERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLIQTIESVRNVEGVLAVSLVYHQQEEQGEETP--------  -
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --NapD-2jsxA01 A:3-82                                                             ------------- Pfam domains
         Sec.struct. author .....eeeeeeeee...hhhhhhhhhh....eeeeeee....eeeeeeee.hhhhhhhhhhhhh....eeeeee..................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                  2jsx A  1 MHTNWQVCSLVVQAKSERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLIQTIESVRNVEGVLAVSLVYHQQEEQGEETPRSHHHHHH 95
                                    10        20        30        40        50        60        70        80        90

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 (1, 1)

Gene Ontology (4, 4)

NMR Structure(hide GO term definitions)

Chain A (NAPD_ECOLI | P0A9I5)

molecular function
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005048	signal sequence binding	Interacting selectively and non-covalently with a signal sequence, a specific peptide sequence found on protein precursors or mature proteins that dictates where the mature protein is localized.
biological process
	GO:0051224	negative regulation of protein transport	Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Visualization

Interactive Views

NMR Structure
	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
(no "Ligands, Modified Residues, Ions" information available for 2jsx)

	Sites
(no "Sites" information available for 2jsx)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2jsx)

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ NMR Structure - model 1 PNG format \| NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2jsx
		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
	NAPD_ECOLI \| P0A9I5
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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
	NAPD_ECOLI \| P0A9I5
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description