1TYY - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF AMINOIMIDAZOLE RIBOSIDE KINASE FROM SALMONELLA ENTERICA

Authors :   Y. Zhang, M. Dougherty, D. M. Downs, S. E. Ealick

Date :   08 Jul 04 (Deposition) - 07 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A,B

Keywords :   Ribokinase Fold, Alpha/Beta, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Zhang, M. Dougherty, D. M. Downs, S. E. Ealick
Crystal Structure Of An Aminoimidazole Riboside Kinase From Salmonella Enterica; Implications For The Evolution Of The Ribokinase Superfamily
Structure V. 12 1809 2004
PubMed-ID: 15458630 | Reference-DOI: 10.1016/J.STR.2004.07.020
(for further references see the PDB file header)

Molecule 1 - PUTATIVE SUGAR KINASE
	Chains	:	A, B
	EC Number	:	2.7.1.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET14B
	Expression System Strain	:	B834(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	STM4066
	Organism Scientific	:	SALMONELLA TYPHIMURIUM LT2
	Organism Taxid	:	99287
	Strain	:	CT18

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 12)

No.	Name	Count	Type	Full Name
1	K	4	Ligand/Ion	POTASSIUM ION
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:246 , THR A:248 , ALA A:287 , GLY A:292	BINDING SITE FOR RESIDUE K A 404
2	AC2	SOFTWARE	ALA A:180 , ALA A:181 , ALA A:183 , GLY A:213	BINDING SITE FOR RESIDUE K A 405
3	AC3	SOFTWARE	ALA B:180 , ALA B:181 , ALA B:183 , GLY B:213	BINDING SITE FOR RESIDUE K B 504
4	AC4	SOFTWARE	ASP B:246 , THR B:248 , ALA B:287	BINDING SITE FOR RESIDUE K B 505

(no "SS Bond" information available for 1TYY)

(no "Cis Peptide Bond" information available for 1TYY)

(no "SAP(SNP)/Variant" information available for 1TYY)

(no "PROSITE Motif" information available for 1TYY)

(no "Exon" information available for 1TYY)

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:297
 aligned with Q8ZKR2_SALTY | Q8ZKR2 from UniProtKB/TrEMBL  Length:319

    Alignment length:304
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304    
         Q8ZKR2_SALTY     5 NKVWVIGDASVDLVPEKQNSYLKCPGGASANVGVCVARLGGECGFIGCLGDDDAGRFLRQVFQDNGVDVTFLRLDADLTSAVLIVNLTADGERSFTYLVHPGADTYVSPQDLPPFRQYEWFYFSSIGLTDRPAREACLEGARRMREAGGYVLFDVNLRSKMWGNTDEIPELIARSAALASICKVSADELCQLSGASHWQDARYYLRDLGCDTTIISLGADGALLITAEGEFHFPAPRVDVVDTTGAGDAFVGGLLFTLSRANCWDHALLAEAISNANACGAMAVTAKGAMTALPFPDQLNTFLS 308
               SCOP domains d1tyya_ A: Aminoimidazole riboside kinase                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1tyyA00 A:5-308  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeee....eeeeeeehhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhh..ee...eee.......eee..-------..ee....hhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhh.hhhhhhhhhhhhhhhh.eeeeehhhhhhhhh..hhhhhh..hhhhh...eeee.hhh.eeee....eeee...........hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tyy A   5 NKVWVIGDASVDLVPEKQNSYLKCPGGASANVGVCVARLGGECGFIGCLGDDDAGRFLRQVFQDNGVDVTFLRLDADLTSAVLIVN-------SFTYLVHPGADTYVSPQDLPPFRQYEWFYFSSIGLTDRPAREACLEGARRmREAGGYVLFDVNLRSKmWGNTDEIPELIARSAALASICKVSADELCQLSGASHWQDARYYLRDLGCDTTIISLGADGALLITAEGEFHFPAPRVDVVDTTGAGDAFVGGLLFTLSRANCWDHALLAEAISNANACGAmAVTAKGAmTALPFPDQLNTFLS 308
                                    14        24        34        44        54        64        74        84     |   -   |   104       114       124       134       144   |   154       164|      174       184       194       204       214       224       234       244       254       264       274       284 |     294       304    
                                                                                                                90      98                                               148-MSE          165-MSE                                                                                                                  286-MSE 294-MSE

Chain B from PDB  Type:PROTEIN  Length:296
 aligned with Q8ZKR2_SALTY | Q8ZKR2 from UniProtKB/TrEMBL  Length:319

    Alignment length:306
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304      
         Q8ZKR2_SALTY     5 NKVWVIGDASVDLVPEKQNSYLKCPGGASANVGVCVARLGGECGFIGCLGDDDAGRFLRQVFQDNGVDVTFLRLDADLTSAVLIVNLTADGERSFTYLVHPGADTYVSPQDLPPFRQYEWFYFSSIGLTDRPAREACLEGARRMREAGGYVLFDVNLRSKMWGNTDEIPELIARSAALASICKVSADELCQLSGASHWQDARYYLRDLGCDTTIISLGADGALLITAEGEFHFPAPRVDVVDTTGAGDAFVGGLLFTLSRANCWDHALLAEAISNANACGAMAVTAKGAMTALPFPDQLNTFLSSH 310
               SCOP domains d1tyyb_ B: Aminoimidazole riboside kinase                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1tyyB00 B:5-310  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                              CATH domains
           Pfam domains (1) PfkB-1tyyB01 B:5-300                                                                                                                                                                                                                                                                                    ---------- Pfam domains (1)
           Pfam domains (2) PfkB-1tyyB02 B:5-300                                                                                                                                                                                                                                                                                    ---------- Pfam domains (2)
         Sec.struct. author ..eeee...eeeeee....eeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhh..ee...eeee......eee..--------.......hhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhh.eeeeehhhhhhhhh..hhhhhh..hhhhh...eeeeee..eeeeee..eeeee...........hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.--.....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tyy B   5 NKVWVIGDASVDLVPEKQNSYLKCPGGASANVGVCVARLGGECGFIGCLGDDDAGRFLRQVFQDNGVDVTFLRLDADLTSAVLIVN--------FTYLVHPGADTYVSPQDLPPFRQYEWFYFSSIGLTDRPAREACLEGARRmREAGGYVLFDVNLRSKmWGNTDEIPELIARSAALASICKVSADELCQLSGASHWQDARYYLRDLGCDTTIISLGADGALLITAEGEFHFPAPRVDVVDTTGAGDAFVGGLLFTLSRANCWDHALLAEAISNANACGAmAVTAK--mTALPFPDQLNTFLSSH 310
                                    14        24        34        44        54        64        74        84     |   -    |  104       114       124       134       144   |   154       164|      174       184       194       204       214       224       234       244       254       264       274       284 |    |294       304      
                                                                                                                90       99                                              148-MSE          165-MSE                                                                                                                  286-MSE1  |                
                                                                                                                                                                                                                                                                                                                           294-MSE

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Ribokinase-like (226)

Superfamily: Ribokinase-like (189)

Family: Ribokinase-like (36)

Protein domain: Aminoimidazole riboside kinase (3)

Salmonella typhimurium [TaxId: 90371] (3)

1a	d1tyya_	A:
1b	d1tyyb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (109)

Homologous Superfamily: [code=3.40.1190.20, no name defined] (73)

Salmonella typhimurium lt2. Organism_taxid: 99287. Strain: ct18. (3)

1a	1tyyB00	B:5-310
1b	1tyyA00	A:5-308

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ribokinase (55)

Family: PfkB (39)

Salmonella typhimurium (3)

1a	PfkB-1tyyB01	B:5-300
1b	PfkB-1tyyB02	B:5-300

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q8ZKR2_SALTY | Q8ZKR2)

molecular function
	GO:0008715	CDP-diacylglycerol diphosphatase activity	Catalysis of the reaction: CDP-diacylglycerol + H(2)O = a phosphatidate + CMP + 2 H(+).
	GO:0008865	fructokinase activity	Catalysis of the reaction: ATP + D-fructose = ADP + D-fructose 6-phosphate.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	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:0004747	ribokinase activity	Catalysis of the reaction: ATP + D-ribose = ADP + D-ribose 5-phosphate.
	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:0006014	D-ribose metabolic process	The chemical reactions and pathways involving D-ribose (ribo-pentose). As beta-D-ribofuranose, D-ribose forms the glycose group of all ribonucleosides, ribonucleotides and ribonucleic acids, and also of ribose phosphates, various glycosides, some coenzymes and some forms of vitamin B12.
	GO:0046835	carbohydrate phosphorylation	The process of introducing a phosphate group into a carbohydrate, any organic compound based on the general formula Cx(H2O)y.
	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.

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
		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1tyy)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites 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)

Access by PDB/NDB ID
	1tyy
		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
	Q8ZKR2_SALTY \| Q8ZKR2
		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)
	2.7.1.4
		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

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
	Q8ZKR2_SALTY \| Q8ZKR2
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q8ZKR2_SALTY \| Q8ZKR2	:	1tz3 1tz6

(no "Related Entries Specified in the PDB File" available for 1TYY)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (4, 4)

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

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (11, 11)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File