3L84 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   HIGH RESOLUTION CRYSTAL STRUCTURE OF TRANSKETOLASE FROM CAMPYLOBACTER JEJUNI SUBSP. JEJUNI NCTC 11168

Authors :   B. Nocek, M. Makowska-Grzyska, N. Maltseva, S. Grimshaw, W. Anderson, A. Joachimiak

Date :   29 Dec 09 (Deposition) - 09 Feb 10 (Release) - 22 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.36

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

Keywords :   Transketolase, Tkt, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Nocek, M. Makowska-Grzysa, N. Maltseva, S. Grimshaw, W. F. Anderson, A. Joachimiak
High Resolution Crystal Structure Of Transketolase From Campylobacter Jejuni Subsp. Jejuni Nctc 11168
To Be Published
PubMed: search

Molecule 1 - TRANSKETOLASE
	Chains	:	A
	EC Number	:	2.2.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21(DE3)-MAGIC
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TKT, CJ1645
	Organism Scientific	:	CAMPYLOBACTER JEJUNI
	Organism Taxid	:	192222
	Strain	:	SUBSP. JEJUNI NCTC 11168

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 24)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	GOL	4	Ligand/Ion	GLYCEROL
3	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:9 , SER A:43 , ARG A:289 , PHE A:290 , SER A:292 , ALA A:293 , LEU A:296 , HOH A:932	BINDING SITE FOR RESIDUE GOL A 2001
2	AC2	SOFTWARE	HIS A:77 , LYS A:287 , GLU A:291 , HOH A:874 , HOH A:1303	BINDING SITE FOR RESIDUE GOL A 2002
3	AC3	SOFTWARE	SER A:311 , ALA A:312 , LYS A:313 , LYS A:314 , GLU A:315	BINDING SITE FOR RESIDUE ACT A 3001

(no "SS Bond" information available for 3L84)

Asymmetric Unit

No.	Residues
1	Phe A:379	-	Val A:380

(no "SAP(SNP)/Variant" information available for 3L84)

(no "PROSITE Motif" information available for 3L84)

(no "Exon" information available for 3L84)

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:632
 aligned with Q0P7Y3_CAMJE | Q0P7Y3 from UniProtKB/TrEMBL  Length:632

    Alignment length:632
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630  
         Q0P7Y3_CAMJE     1 MNIQILQEQANTLRFLSADMVQKANSGHPGAPLGLADILSVLSYHLKHNPKNPTWLNRDRLVFSGGHASALLYSFLHLSGYDLSLEDLKNFRQLHSKTPGHPEISTLGVEIATGPLGQGVANAVGFAMAAKKAQNLLGSDLIDHKIYCLCGDGDLQEGISYEACSLAGLHKLDNFILIYDSNNISIEGDVGLAFNENVKMRFEAQGFEVLSINGHDYEEINKALEQAKKSTKPCLIIAKTTIAKGAGELEGSHKSHGAPLGEEVIKKAKEQAGFDPNISFHIPQASKIRFESAVELGDLEEAKWKDKLEKSAKKELLERLLNPDFNKIAYPDFKGKDLATRDSNGEILNVLAKNLEGFLGGSADLGPSNKTELHSMGDFVEGKNIHFGIREHAMAAINNAFARYGIFLPFSATFFIFSEYLKPAARIAALMKIKHFFIFTHDSIGVGEDGPTHQPIEQLSTFRAMPNFLTFRPADGVENVKAWQIALNADIPSAFVLSRQKLKALNEPVFGDVKNGAYLLKESKEAKFTLLASGSEVWLCLESANELEKQGFACNVVSMPCFELFEKQDKAYQERLLKGEVIGVEAAHSNELYKFCHKVYGIESFGESGKDKDVFERFGFSVSKLVNFILSK 632
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3l84A01 A:2-318  [code=3.40.50.970, no name defined]                                                                                                                                                                                                                                                                         3l84A02 A:319-514  [code=3.40.50.970, no name defined]                                                                                                                                              3l84A03 A:515-632  [code=3.40.50.920, no name defined]                                                                 CATH domains
               Pfam domains ----Transketolase_N-3l84A02 A:5-325                                                                                                                                                                                                                                                                                                  ----------Transket_pyr-3l84A01 A:336-504                                                                                                                                           ------------Transketolase_C-3l84A03 A:517-625                                                                            ------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh................eeee.hhhhhhhhhhhhhhhh...hhhhhh...........................hhhhhhhhhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhhhhhhh....eeeeeee..ee..ee.hhh...hhhhhhhhh..eeeeee..hhhhhhhhhhhhhh....eeeeee......hhhhh.hhhhh....hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh................hhhhhhhhhhhhhhhhh..eeeee..hhhhhh.............eee...hhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhh...eeeee..hhhhh..hhhhh..hhhhhhhhh...eee...hhhhhhhhhhhhhhh...eeee...............hhhhh.eeee......eeeee...hhhhhhhhhhhhhhh...eeeee..hhhhhhh.hhhhhhhhh..eeeee....hhhhhhh..eee.........hhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l84 A   1 mNIQILQEQANTLRFLSADmVQKANSGHPGAPLGLADILSVLSYHLKHNPKNPTWLNRDRLVFSGGHASALLYSFLHLSGYDLSLEDLKNFRQLHSKTPGHPEISTLGVEIATGPLGQGVANAVGFAmAAKKAQNLLGSDLIDHKIYCLCGDGDLQEGISYEACSLAGLHKLDNFILIYDSNNISIEGDVGLAFNENVKmRFEAQGFEVLSINGHDYEEINKALEQAKKSTKPCLIIAKTTIAKGAGELEGSHKSHGAPLGEEVIKKAKEQAGFDPNISFHIPQASKIRFESAVELGDLEEAKWKDKLEKSAKKELLERLLNPDFNKIAYPDFKGKDLATRDSNGEILNVLAKNLEGFLGGSADLGPSNKTELHSmGDFVEGKNIHFGIREHAmAAINNAFARYGIFLPFSATFFIFSEYLKPAARIAALmKIKHFFIFTHDSIGVGEDGPTHQPIEQLSTFRAmPNFLTFRPADGVENVKAWQIALNADIPSAFVLSRQKLKALNEPVFGDVKNGAYLLKESKEAKFTLLASGSEVWLCLESANELEKQGFACNVVSmPCFELFEKQDKAYQERLLKGEVIGVEAAHSNELYKFCHKVYGIESFGESGKDKDVFERFGFSVSKLVNFILSK 632
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370     | 380       390   |   400       410       420       430|      440       450       460    |  470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630  
                            |                 20-MSE                                                                                                     128-MSE                                                                 200-MSE                                                                                                                                                                         376-MSE           394-MSE                              431-MSE                           465-MSE                                                                                       559-MSE                                                                     
                            1-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 '\|'

(no "SCOP Domain" information available for 3L84)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: THDP-binding (106)

Family: Transket_pyr (45)

Campylobacter jejuni (4)

Transket_pyr-3l84A01

A:336-504

Family: Transketolase_N (22)

Campylobacter jejuni (4)

Transketolase_N-3l84A02

A:5-325

Clan: no clan defined [family: Transketolase_C] (40)

Family: Transketolase_C (40)

Campylobacter jejuni (4)

Transketolase_C-3l84A03

A:517-625

Asymmetric Unit(hide GO term definitions)

Chain A (Q0P7Y3_CAMJE | Q0P7Y3)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
	GO:0004802	transketolase activity	Catalysis of the reversible transfer of a 2-carbon ketol group (CH2OH-CO-) from a ketose phosphate donor to an aldose phosphate acceptor.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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

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

	Cis Peptide Bonds
		Phe A:379 - Val A:380	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - 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
	3l84
		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
	Q0P7Y3_CAMJE \| Q0P7Y3
		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)
	2.2.1.1
		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
	Q0P7Y3_CAMJE \| Q0P7Y3
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q0P7Y3_CAMJE \| Q0P7Y3	:	3m34 3m6l 3m7i

(no "Related Entries Specified in the PDB File" available for 3L84)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (3, 3)

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

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (2, 3)

Pfam Domains (3, 3)

Gene Ontology (5, 5)

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