3WNM - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   D308A MUTANT OF BACILLUS CIRCULANS T-3040 CYCLOISOMALTOOLIGOSACCHARIDE GLUCANOTRANSFERASE COMPLEXED WITH ISOMALTOHEPTAOSE

Authors :   N. Suzuki, Z. Fujimoto, Y. M. Kim, M. Momma, N. Kishine, R. Suzuki, S. Suz S. Kitamura, M. Kobayashi, A. Kimura, K. Funane

Date :   10 Dec 13 (Deposition) - 05 Feb 14 (Release) - 04 Mar 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

Chains :   Asym./Biol. Unit : A

Keywords :   C2 Type Immunoglobulin Fold, (Beta/Alpha)8-Barrel, Beta-Jelly Roll, Greek Key, Glycoside Hydrolase, Alpha-1, 6-Glucan, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Suzuki, Z. Fujimoto, Y. M. Kim, M. Momma, N. Kishine, R. Suzuki, S. Suzuki, S. Kitamura, M. Kobayashi, A. Kimura, K. Funane
Structural Elucidation Of The Cyclization Mechanism Of Alpha-1, 6-Glucan By Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase.
J. Biol. Chem. V. 289 12040 2014
PubMed-ID: 24616103 | Reference-DOI: 10.1074/JBC.M114.547992
(for further references see the PDB file header)

Molecule 1 - CYCLOISOMALTOOLIGOSACCHARIDE GLUCANOTRANSFERASE
	Chains	:	A
	EC Number	:	2.4.1.248
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 39-738
	Gene	:	CIT
	Mutation	:	YES
	Organism Scientific	:	BACILLUS CIRCULANS
	Organism Taxid	:	1397
	Strain	:	T-3040

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 22)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
2	CA	1	Ligand/Ion	CALCIUM ION
3	GLC	10	Ligand/Ion	ALPHA-D-GLUCOSE
4	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5	NA	1	Ligand/Ion	SODIUM ION
6	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:424 , GLU A:426 , THR A:443 , GLY A:446 , ASP A:541	BINDING SITE FOR RESIDUE CA A 801
02	AC2	SOFTWARE	ASP A:664 , GLN A:666 , ASN A:669 , HOH A:1115 , HOH A:1128	BINDING SITE FOR RESIDUE NA A 802
03	AC3	SOFTWARE	ARG A:53 , ASN A:55 , LYS A:229 , HOH A:1122 , HOH A:1332	BINDING SITE FOR RESIDUE SO4 A 803
04	AC4	SOFTWARE	PRO A:113 , SER A:114 , HOH A:1158	BINDING SITE FOR RESIDUE SO4 A 804
05	AC5	SOFTWARE	THR A:159 , ALA A:160 , HOH A:1230	BINDING SITE FOR RESIDUE SO4 A 805
06	AC6	SOFTWARE	ASN A:345 , ARG A:348 , HOH A:1143 , HOH A:1155	BINDING SITE FOR RESIDUE SO4 A 806
07	AC7	SOFTWARE	ALA A:416 , ARG A:475 , TRP A:509 , HIS A:511	BINDING SITE FOR RESIDUE SO4 A 807
08	AC8	SOFTWARE	GLN A:169 , ASN A:574 , LYS A:594	BINDING SITE FOR RESIDUE SO4 A 808
09	AC9	SOFTWARE	TRP A:186 , LYS A:193 , LEU A:204 , HOH A:1047 , HOH A:1119 , HOH A:1181	BINDING SITE FOR RESIDUE SO4 A 809
10	BC1	SOFTWARE	TYR A:530 , VAL A:535 , GLY A:536 , GLC A:819 , HOH A:1346	BINDING SITE FOR RESIDUE SO4 A 810
11	BC2	SOFTWARE	ARG A:123 , GLN A:131 , GLY A:132 , LYS A:598 , ASP A:599 , ASN A:602 , SER A:703 , GLY A:704	BINDING SITE FOR RESIDUE MES A 811
12	BC3	SOFTWARE	TYR A:182 , ASP A:183 , MET A:185 , HIS A:188 , PHE A:207 , TYR A:233 , MET A:235 , GLU A:256 , ASN A:262 , ASP A:267 , PHE A:268 , ALA A:308 , GLN A:309 , MET A:310 , GLN A:312 , ARG A:313 , ASN A:354 , ASP A:357 , GLU A:380 , TRP A:382 , GLU A:580 , TYR A:581 , TYR A:582 , HOH A:1028 , HOH A:1029 , HOH A:1052 , HOH A:1056 , HOH A:1082 , HOH A:1152 , HOH A:1156 , HOH A:1172 , HOH A:1223 , HOH A:1224 , HOH A:1227 , HOH A:1264 , HOH A:1341	BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 812 TO 818
13	BC4	SOFTWARE	HIS A:439 , GLN A:450 , ALA A:452 , THR A:480 , TRP A:506 , ALA A:537 , ASN A:539 , SO4 A:810 , HOH A:1290 , HOH A:1346	BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 819 TO 822

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

(no "Cis Peptide Bond" information available for 3WNM)

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CBM6	PS51175	CBM6 (carbohydrate binding type-6) domain profile.	CTA1_BACCI	421-546 748-871	1	A:421-546 -

(no "Exon" information available for 3WNM)

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:701
 aligned with CTA1_BACCI | P94286 from UniProtKB/Swiss-Prot  Length:972

    Alignment length:701
                                    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       640       650       660       670       680       690       700       710       720       730       740 
           CTA1_BACCI    41 SGGIERVFTDKARYNPGDAVSIRVQAKNGTGSSWSGAARLEIFHLENSVYTSSQSLSLTNGQSTTLTFTWTAPSTDFRGYFVRIDAGTLGQGATAIDVSSDFTKYPRYGYISEFESGETALESKAKVDQLAQDYHINAWQFYDWMWRHDKMIKRTGGSIDSTWLDLFNREISWSTLQNQIDAVHDVNGKAMAYAMIYASRENYSPLGISPTWGIYEDSSHTNQFDVDFGDGSTYLYMSDPQNPNWQNYIHAEYIDSINTAGFDGIHVDQMGQRSNVYDYNGNSIDLSTRFSPFLDQAKSVLSANNPARDNLTYNIVDGTVNGWAVNDVSKNADLDFLYSEIWYLSDSYNQLKNYIEQLRANGGNKAVVLAAYMNYADNAGTRYEAESASMTNVSTNTNHAGYTGSGFVDQFASTGDKVSFAINAPEAGDYSLVFRYGNNTGANSTLNLYVDGNFVQKLYFFNQSSWGTWKHDAWYQVPLTQGAHTVELRYESGNVGAVNLDSLTLGTFDEHSVRLADAMMSASGATHIELGDDNQMLPHEYYPNRSKTMRSSLKNAMKDHYNFITAYENLLFDSDVVPNDTGSQFVNLTGVSASGDGSANTVWYINKRTSDYNIVHLINLLGNDNQWRNTASQPSFQTNLPAKIYIGADETISDVYLASPDLSGGETQELAFTSGTDAGGKYVSFTVPELKYWNMIYMKRT 741
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.........eeeeeeeee......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeee......eeeeeeee.hhh.eeeeeeee..hhhhh..eeee.......hhhhhhhhhhhhhhhhh..eeee............ee..ee..eee.....eeehhhhhhhhhhhhhh..eeeeeee..eee..hhhhh.hhhhh...........eee......eeee....hhhhhhhhhhhhhhhhhhhh..eeeee.......ee.....eehhhhhhhhhhhhhhhhhhhhh....eeeeeee.......hhhhhhhhh....eeee......hhhhhhhhhhhhhhhh....eeee.........eeeee.hhheee...ee..........eeeee.....eeeeeeee...eeeeeeeeee......eeeeeee..eeeeeeee.........eeeeeeeeee..eeeeeeee........eeeeeeeee..hhhhhhhhhhhhhhhh.ee..ee...ee.............hhhhhhhhhhhhhhhhhhhhhhh....ee.......eee....ee.......eeeeeee...eeeeeeee.................eeeeeeeee........eeeee...hhhhh.eee..eeeee..eeeeeeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CBM6  PDB: A:421-546 UniProt: 421-546                                                                                         --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wnm A  41 SGGIERVFTDKARYNPGDAVSIRVQAKNGTGSSWSGAARLEIFHLENSVYTSSQSLSLTNGQSTTLTFTWTAPSTDFRGYFVRIDAGTLGQGATAIDVSSDFTKYPRYGYISEFESGETALESKAKVDQLAQDYHINAWQFYDWMWRHDKMIKRTGGSIDSTWLDLFNREISWSTLQNQIDAVHDVNGKAMAYAMIYASRENYSPLGISPTWGIYEDSSHTNQFDVDFGDGSTYLYMFDPQNPNWQNYIHAEYIDSINTAGFDGIHVAQMGQRSNVYDYNGNSIDLSTRFSPFLDQAKSVLSANNPARDNLTYNIVDGTVNGWAVNDVSKNADLDFLYSEIWYLSDSYNQLKNYIEQLRANGGNKAVVLAAYMNYADNAGTRYEAESASMTNVSTNTNHAGYTGSGFVDQFASTGDKVSFAINAPEAGDYSLVFRYGNNTGANSTLNLYVDGNFVQKLYFFNQSSWGTWKHDAWYQVPLTQGAHTVELRYESGNVGAVNLDSLTLGTFDEHSVRLADAMMSASGATHIELGDDNQMLPHEYYPNRSKTMRSSLKNAMKDHYNFITAYENLLFDSDVVPNDTGSQFVNLTGVSASGDGSANTVWYINKRTSDYNIVHLINLLGNDNQWRNTASQPSFQTNLPAKIYIGADETISDVYLASPDLSGGETQELAFTSGTDAGGKYVSFTVPELKYWNMIYMLEH 741
                                    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       640       650       660       670       680       690       700       710       720       730       740

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 3WNM)

(no "CATH Domain" information available for 3WNM)

(no "Pfam Domain" information available for 3WNM)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CTA1_BACCI | P94286)


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: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).

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
		BGC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GLC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MES	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]

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

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
	3wnm
		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
	CTA1_BACCI \| P94286
		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)
	2.4.1.248
		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
	CTA1_BACCI \| P94286
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	CTA1_BACCI \| P94286	:	3wnk 3wnl 3wnn 3wno 3wnp

3wnk	THE SAME PROTEIN WITHOUT MUTAION
3wnl	THE SAME PROTEIN COMPLEXED WITH ISOMALTOHEXAOSE
3wnn	THE SAME PROTEIN COMPLEXED WITH ISOMALTOOCTAOSE
3wno	THE SAME PROTEIN COMPLEXED WITH CYCLOISOMALTOOCTAOSE
3wnp	THE SAME PROTEIN COMPLEXED WITH ISOMALTOUNDECAOSE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 22)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (3, 3)

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