3K8U - JenaLib

Title :   CRYSTAL STRUCTURE OF THE PEPTIDASE DOMAIN OF STREPTOCOCCUS COMA, A BI-FUNCTIONAL ABC TRANSPORTER INVOLVED IN QUORUM SENSING PATHWAY

Authors :   S. Ishii, T. Yano, A. Ebihara, A. Okamoto, M. Manzoku, H. Hayashi

Date :   14 Oct 09 (Deposition) - 23 Feb 10 (Release) - 26 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Abc Transporter, Coma, Cysteine Protease, Quorum-Sensing, Streptococcus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Ishii, T. Yano, A. Ebihara, A. Okamoto, M. Manzoku, H. Hayashi
Crystal Structure Of The Peptidase Domain Of Streptococcus Coma, A Bifunctional Atp-Binding Cassette Transporter Involved In The Quorum-Sensing Pathway
J. Biol. Chem. V. 285 10777 2010
PubMed-ID: 20100826 | Reference-DOI: 10.1074/JBC.M109.093781

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:137
 aligned with Q8DW05_STRMU | Q8DW05 from UniProtKB/TrEMBL  Length:760

    Alignment length:137
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       
         Q8DW05_STRMU    49 HYKLVPQIDTRDCGPAVLASVAKHYGSNYSIAYLRELSKTNKQGTTALGIVEAAKKLGFETRSIKADMTLFDYNDLTYPFIVHVIKGKRLQHYYVVYGSQNNQLIIGDPDPSVKVTRMSKERFQSEWTGLAIFLAPQ 185
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Peptidase_C39-3k8uA01 A:5-141                                                                                                             Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhh....hhhhhhhhh.......hhhhhhhhhhhh.eeeeeee.hhhhhhh......eeeeeee..eeeeeeeeeeee..eeeeee.....eeeeeehhhhhhheeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k8u A   5 HYKLVPQIDTRDCGPAVLASVAKHYGSNYSIAYLRELSKTNKQGTTALGIVEAAKKLGFETRSIKADMTLFDYNDLTYPFIVHVIKGKRLQHYYVVYGSQNNQLIIGDPDPSVKVTRMSKERFQSEWTGLAIFLAPQ 141
                                    14        24        34        44        54        64        74        84        94       104       114       124       134

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 (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q8DW05_STRMU | Q8DW05)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	GO:0042626	ATPase activity, coupled to transmembrane movement of substances	Catalysis of the reaction: ATP + H2O = ADP + phosphate, to directly drive the active transport of a substance across a membrane.
	GO:0022885	bacteriocin transmembrane transporter activity	Enables the transfer of a bacteriocin from one side of the membrane to the other.
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	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:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
	GO:0043213	bacteriocin transport	The directed movement of a bacteriocin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Bacteriocins are a group of antibiotics produced by bacteria and are encoded by a group of naturally occurring plasmids, e.g. Col E1. Bacteriocins are toxic to bacteria closely related to the bacteriocin producing strain.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Visualization

Interactive Views

Asymmetric/Biological 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
(no "Ligands, Modified Residues, Ions" information available for 3k8u)

	Sites
(no "Sites" information available for 3k8u)

	Cis Peptide Bonds
		Tyr A:82 - Pro A:83	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3k8u
		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
	Q8DW05_STRMU \| Q8DW05
		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
	Q8DW05_STRMU \| Q8DW05
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description