3JUL - JenaLib

Title :   CRYSTAL STRUCTURE OF LISTERIA INNOCUA D-TAGATOSE-6-PHOSPHATE KINASE BOUND WITH SUBSTRATE

Authors :   L. Satyanarayana, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   15 Sep 09 (Deposition) - 06 Oct 09 (Release) - 01 Dec 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Kinase, Atp, Transferase, Listeria Innocua, Tagatose-6- Phosphate, Mg+2 Ion, 11206N1, Psi-Ii, Nysgxrc, Atp-Binding, Nucleotide-Binding, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Satyanarayana, S. K. Burley, S. Swaminathan
Crystal Structure Of Listeria Innocua D-Tagatose-6-Phosphate Kinase Bound With Substrate
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (2, 2)

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:298
 aligned with Q929S5_LISIN | Q929S5 from UniProtKB/TrEMBL  Length:310

    Alignment length:309
                             1                                                                                                                                                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299         
         Q929S5_LISIN     - -MIYTITLNPAIDRLLFIRGELEKRKTNRVIKTEFDCGGKGLHVSGVLSKFGIKNEALGIAGSDNLDKLYAILKEKHINHDFLVEAGTSTRECFVVLSDDTNGSTMIPEAGFTVSQTNKDNLLKQIAKKVKKEDMVVIAGSPPPHYTLSDFKELLRTVKATGAFLGCDNSGEYLNLAVEMGVDFIKPNEDEVIAILDEKTNSLEENIRTLAEKIPYLVVSLGAKGSICAHNGKLYQVIPPKVQERNDTGAGDVFVGAFIAGLAMNMPITETLKVATGCSASKVMQQDSSSFDLEAAGKLKNQVSIIQLE 308
               SCOP domains d3jula_ A: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----PfkB-3julA01 A:5-295                                                                                                                                                                                                                                                                               ------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeeee..............eeeeeeehhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhh......eee.....eeeeeee.......eeee......hhhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh..ee..hhhhhhhhhh....hhhhhhhhhhh...eeeee.hhh.eeeee..eeeeee..-------.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...----.hhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jul A  -2 SLIYTITLNPAIDRLLFIRGELEKRKTNRVIKTEFDCGGKGLHVSGVLSKFGIKNEALGIAGSDNLDKLYAILKEKHINHDFLVEAGTSTRECFVVLSDDTNGSTmIPEAGFTVSQTNKDNLLKQIAKKVKKEDmVVIAGSPPPHYTLSDFKELLRTVKATGAFLGCDNSGEYLNLAVEmGVDFIKPNEDEVIAILDEKTNSLEENIRTLAEKIPYLVVSLGAKGSICAHNGKLYQVIPP-------TGAGDVFVGAFIAGLAmNmPITETLKVATGCSASKVmQQ----FDLEAAGKLKNQVSIIQLE 308
                             ||      9        19        29        39        49        59        69        79        89        99     | 109       119       129    |  139       149       159       169       179       189       199       209       219       229       239       249       259   | | 269       279   | |   -|      299         
                             ||                                                                                                    105-MSE                      134-MSE                                      179-MSE                                                     239     247             263-MSE             283-MSE290                  
                            -1|                                                                                                                                                                                                                                                                    265-MSE             285                       
                              2

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 (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A (Q929S5_LISIN | Q929S5)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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:0016773	phosphotransferase activity, alcohol group as acceptor	Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
	GO:0009024	tagatose-6-phosphate kinase activity	Catalysis of the reaction: ATP + D-tagatose 6-phosphate = ADP + D-tagatose 1,6-bisphosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:2001059	D-tagatose 6-phosphate catabolic process	The chemical reactions and pathways resulting in the breakdown of a D-tagatose 6-phosphate.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0005988	lactose metabolic process	The chemical reactions and pathways involving lactose, the disaccharide galactopyranosyl-glucose.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

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
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TA6	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3jul)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3jul
		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
	Q929S5_LISIN \| Q929S5
		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)
	2.7.1.144
		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

Description