1K1W - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF 4-ALPHA-GLUCANOTRANSFERASE FROM THERMOCOCCUS LITORALIS

Authors :   H. Imamura, S. Fushinobu, T. Kumasaka, M. Yamamoto, B. S. Jeon, T. Wakagi, H. Matsuzawa

Date :   26 Sep 01 (Deposition) - 17 Jun 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A

Keywords :   4-Alpha-Glucanotransferase, Seleno-Methionine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Imamura, S. Fushinobu, M. Yamamoto, T. Kumasaka, B. S. Jeon, T. Wakagi, H. Matsuzawa
Crystal Structures Of 4-Alpha-Glucanotransferase From Thermococcus Litoralis And Its Complex With An Inhibitor
J. Biol. Chem. V. 278 19378 2003
PubMed-ID: 12618437 | Reference-DOI: 10.1074/JBC.M213134200
(for further references see the PDB file header)

Molecule 1 - 4-ALPHA-GLUCANOTRANSFERASE
	Chains	:	A
	EC Number	:	2.4.1.25
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUT7
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMOCOCCUS LITORALIS
	Organism Taxid	:	2265

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 16)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	GLC	1	Ligand/Ion	ALPHA-D-GLUCOSE
3	MSE	13	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:124 , ARG A:182 , ASP A:213 , ASP A:214 , TYR A:272 , TRP A:278 , VAL A:360 , HIS A:464	BINDING SITE FOR RESIDUE GLC A 660
2	AC2	SOFTWARE	ASP A:392 , ASP A:394 , ASP A:396 , ARG A:398 , GLU A:400	BINDING SITE FOR RESIDUE CA A 661
3	AC3	SOFTWARE	PRO A:94 , LYS A:335 , ARG A:338	BINDING SITE FOR RESIDUE SO4 A 662

(no "SS Bond" information available for 1K1W)

Asymmetric/Biological Unit

No.	Residues
1	Ile A:185	-	Pro A:186

(no "SAP(SNP)/Variant" information available for 1K1W)

(no "PROSITE Motif" information available for 1K1W)

(no "Exon" information available for 1K1W)

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:628
 aligned with MALQ_THELN | O32462 from UniProtKB/Swiss-Prot  Length:659

    Alignment length:656
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653      
           MALQ_THELN     4 INFIFGIHNHQPLGNFGWVFEEAYNRSYRPFMEILEEFPEMKVNVHFSGPLLEWIEENKPDYLDLLRSLIKRGQLEIVVAGFYEPVLAAIPKEDRLVQIEMLKDYARKLGYDAKGVWLTERVWQPELVKSLREAGIEYVVVDDYHFMSAGLSKEELFWPYYTEDGGEVITVFPIDEKLRYLIPFRPVKKTIEYLESLTSDDPSKVAVFHDDGEKFGVWPGTYEWVYEKGWLREFFDAITSNEKINLMTYSEYLSKFTPRGLVYLPIASYFEMSEWSLPAKQAKLFVEFVEQLKEEGKFEKYRVFVRGGIWKNFFFKYPESNFMHKRMLMVSKAVRDNPEARKYILKAQCNDAYWHGVFGGIYLPHLRRTVWENIIKAQRYLKPENKILDVDFDGRAEIMVENDGFIATIKPHYGGSIFELSSKRKAVNYNDVLPRRWEHYHEVPEATKPEKESEEGIASIHELGKQIPEEIRRELAYDWQLRAILQDHFIKPEETLDNYRLVKYHELGDFVNQPYEYEMIENGVKLWREGGVYAEEKIPARVEKKIELTEDGFIAKYRVLLEKPYKALFGVEINLAVHSVMEKPEEFEAKEFEVNDPYGIGKVRIELDKAAKVWKFPIKTLSQSEAGWDFIQQGVSYTMLFPIEKELEFTVRFREL 659
               SCOP domains d1k1wa3 A:4-310 4-alpha-glucanotransferase, N-terminal domain                                                                                                                                                                                                                                                      d1k1wa1 A:311-384 4-alpha-glucanotransferase, domain 2                    d1k1wa2 A:385-659 4-alpha-glucanotransferase, C-terminal domain                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee......hhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhh...hhhhhhhhh...eeeeehhhhhh...hhhhh...eeeee..eeeeeeee..hhhhhh....hhhhhhhh...-----..eeeeeee.hhh.......-------hhhhhhhhhh--...ee.hhhhhh.................hhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh......eee........eeeee...eeeee.......eeeeee....ee.........hhhhh....--------------.......hhhhhh..........eeeeeee....hhhhhhh..............eeee...eeeeee..eee...eee..eeeeeeee..eeeeeeeee......eeeeeeeee.........eeeeeeeeeee......eeeeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeee..eeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k1w A   4 INFIFGIHNHQPLGNFGWVFEEAYNRSYRPFmEILEEFPEmKVNVHFSGPLLEWIEENKPDYLDLLRSLIKRGQLEIVVAGFYEPVLAAIPKEDRLVQIEmLKDYARKLGYDAKGVWLTERVWQPELVKSLREAGIEYVVVDDYHFmSAGLSKEELFWPYYTEDGGEVITVFPIDEKLRYLIPFRPVKKTIEYLESL-----SKVAVFHDDGEKFGVWPGTY-------WLREFFDAIT--EKINLmTYSEYLSKFTPRGLVYLPIASYFEmSEWSLPAKQAKLFVEFVEQLKEEGKFEKYRVFVRGGIWKNFFFKYPESNFmHKRmLmVSKAVRDNPEARKYILKAQCNDAYWHGVFGGIYLPHLRRTVWENIIKAQRYLKPENKILDVDFDGRAEImVENDGFIATIKPHYGGSIFELSSKRKAVNYNDVLPRRWEHYHEVPEA--------------HELGKQIPEEIRRELAYDWQLRAILQDHFIKPEETLDNYRLVKYHELGDFVNQPYEYEmIENGVKLWREGGVYAEEKIPARVEKKIELTEDGFIAKYRVLLEKPYKALFGVEINLAVHSVmEKPEEFEAKEFEVNDPYGIGKVRIELDKAAKVWKFPIKTLSQSEAGWDFIQQGVSYTmLFPIEKELEFTVRFREL 659
                                    13        23        33 |      43|       53        63        73        83        93       103|      113       123       133       143      |153       163       173       183       193      |  -  |    213       223 |     233        |- |    |253       263       273 |     283       293       303       313       323  |   |333       343       353       363       373       383       393       403       413       423       433       443     |   -         -|      473       483       493       503       513       523       533       543       553       563       573       583|      593       603       613       623       633       643       653      
                                                          35-MSE   44-MSE                                                     104-MSE                                       150-MSE                                           200   206                225     233      242  |    |                      275-MSE                                            326-MSE |                                                                   402-MSE                                        449            464                                                       522-MSE                                                       584-MSE                                                   642-MSE             
                                                                                                                                                                                                                                                                           245    |                                                                             330-MSE                                                                                                                                                                                                                                                                                                                                     
                                                                                                                                                                                                                                                                                250-MSE                                                                           332-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 "CATH Domain" information available for 1K1W)

(no "Pfam Domain" information available for 1K1W)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MALQ_THELN | O32462)

molecular function
	GO:0004134	4-alpha-glucanotransferase activity	Catalysis of the transfer of a segment of a (1->4)-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose or (1->4)-alpha-D-glucan.
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	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: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:0016757	transferase activity, transferring glycosyl groups	Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
	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:0005977	glycogen metabolic process	The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.

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
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GLC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
		Ile A:185 - Pro A:186	[ RasMol ]

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
	1k1w
		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
	MALQ_THELN \| O32462
		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)
	2.4.1.25
		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
	MALQ_THELN \| O32462
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	MALQ_THELN \| O32462	:	1k1x 1k1y

1k1x	1K1X CONTAINS THE SAME PROTEIN WITH 2-AMINO-2-HYDROXYMETHYL -PROPANE-1,3-DIOL
1k1y	1K1Y CONTAINS THE SAME PROTEIN COMPLEXED WITH ACARBOSE AND MALTOSE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 16)

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 (3, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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