3WAU - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF 4-O-BETA-D-MANNOSYL-D-GLUCOSE PHOSPHORYLASE MGP COMPLEXED WITH M1P

Authors :   S. Nakae, S. Ito, M. Higa, T. Senoura, J. Wasaki, A. Hijikata, M. Shionyu T. Shirai

Date :   08 May 13 (Deposition) - 04 Sep 13 (Release) - 20 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)

Keywords :   5-Bladed Beta Propeller Fold, Phosphorylase, Mannan Biodegradation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Nakae, S. Ito, M. Higa, T. Senoura, J. Wasaki, A. Hijikata, M. Shionyu, S. Ito, T. Shirai
Structure Of Novel Enzyme In Mannan Biodegradation Process 4-O-Beta-D-Mannosyl-D-Glucose Phosphorylase Mgp
J. Mol. Biol. V. 425 4468 2013
PubMed-ID: 23954514 | Reference-DOI: 10.1016/J.JMB.2013.08.002

Molecule 1 - 4-O-BETA-D-MANNOSYL-D-GLUCOSE PHOSPHORYLASE
	Chains	:	A, B
	EC Number	:	2.4.1.281
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-23A(+)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BF0772
	Organism Scientific	:	BACTEROIDES FRAGILIS
	Organism Taxid	:	272559
	Strain	:	NCTC 9343
	Synonym	:	MGP, MANNOSYLGLUCOSE PHOSPHORYLASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	M1P	2	Ligand/Ion	ALPHA-D-MANNOSE 1-PHOSPHATE
2	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	PO4	4	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 24)

No.	Name	Count	Type	Full Name
1	M1P	6	Ligand/Ion	ALPHA-D-MANNOSE 1-PHOSPHATE
2	MPD	6	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	PO4	12	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:311 , GLY A:312 , ARG A:315 , HOH A:535 , HOH A:557 , HOH A:975 , HOH A:1061	BINDING SITE FOR RESIDUE PO4 A 401
2	AC2	SOFTWARE	HIS A:15 , GLU A:16 , LEU A:19 , PRO A:47 , PHE A:49 , ARG A:111 , HOH A:561 , HOH A:921	BINDING SITE FOR RESIDUE PO4 A 402
3	AC3	SOFTWARE	ARG A:88 , ARG A:94 , ARG A:276 , VAL A:319 , ASP A:344 , M1P A:404 , HOH A:610 , HOH A:974	BINDING SITE FOR RESIDUE MPD A 403
4	AC4	SOFTWARE	ASN A:73 , ARG A:88 , ASP A:131 , ARG A:191 , ASN A:192 , ARG A:209 , LYS A:254 , HIS A:273 , TYR A:284 , ASP A:344 , MPD A:403 , HOH A:895 , HOH A:896	BINDING SITE FOR RESIDUE M1P A 404
5	AC5	SOFTWARE	VAL B:311 , GLY B:312 , ARG B:315 , HOH B:562 , HOH B:592 , HOH B:769 , HOH B:898	BINDING SITE FOR RESIDUE PO4 B 401
6	AC6	SOFTWARE	HIS B:15 , GLU B:16 , LEU B:19 , PRO B:47 , PHE B:49 , ARG B:111 , HOH B:571 , HOH B:788 , HOH B:915	BINDING SITE FOR RESIDUE PO4 B 402
7	AC7	SOFTWARE	ARG B:88 , ARG B:94 , ARG B:276 , VAL B:319 , ASP B:344 , M1P B:404 , HOH B:581 , HOH B:969	BINDING SITE FOR RESIDUE MPD B 403
8	AC8	SOFTWARE	ASN B:73 , ARG B:88 , ASP B:131 , ARG B:191 , ASN B:192 , ARG B:209 , HIS B:273 , TYR B:284 , PHE B:324 , ASP B:344 , MPD B:403 , HOH B:816	BINDING SITE FOR RESIDUE M1P B 404

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

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

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

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

(no "Exon" information available for 3WAU)

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:387
 aligned with MGP_BACFN | Q5LH68 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:389
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381         
            MGP_BACFN     2 SLFNDKVAKLLAGHEALLMRKNEPVEEGNGVITRYRYPVLTAAHTPVFWRYDLNEETNPFLMERIGMNATLNAGAIKWDGKYLMLVRVEGADRKSFFAVAESPNGIDNFRFWEYPVTLPEDVVPATNVYDMRLTAHEDGWIYGIFCAERHDDNAPIGDLSSATATAGIARTKDLKNWERLPDLKTKSQQRNVVLHPEFVDGKYALYTRPQDGFIDTGSGGGIGWALIDDITHAEVGEEKIIDKRYYHTIKEVKNGEGPHPIKTPQGWLHLAHGVRNCAAGLRYVLYMYMTSLDDPTRLIASPAGYFMAPVGEERIGDVSNVLFSNGWIADDDGKVFIYYASSDTRMHVATSTIERLVDYCLHTPQDGFSSSASVEILKNLIERNLRLMK 390
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh............ee......hhhhhhhhhhh...............eeeeeeeeeeee..eeeeeeeeee....eeeeeeee.......ee...............eeeeeeeee.....eeeeeeeeee...........eeeeeeeeee......ee........ee...ee........eeeee.ee..--......eeeeeee.hhhhh....eeeeee.........eeee....eee..eeeeeeeeeeee..eeeeeeeeeee.......eee.........hhhhhh......eeeeeeee....eeeeeeee...eeeeeeeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wau A   2 SLFNDKVAKLLAGHEALLMRKNEPVEEGNGVITRYRYPVLTAAHTPVFWRYDLNEETNPFLMERIGMNATLNAGAIKWDGKYLMLVRVEGADRKSFFAVAESPNGIDNFRFWEYPVTLPEDVVPATNVYDMRLTAHEDGWIYGIFCAERHDDNAPIGDLSSATATAGIARTKDLKNWERLPDLKTKSQQRNVVLHPEFVDGKYALYTRPQDG--DTGSGGGIGWALIDDITHAEVGEEKIIDKRYYHTIKEVKNGEGPHPIKTPQGWLHLAHGVRNCAAGLRYVLYMYMTSLDDPTRLIASPAGYFMAPVGEERIGDVSNVLFSNGWIADDDGKVFIYYASSDTRMHVATSTIERLVDYCLHTPQDGFSSSASVEILKNLIERNLRLMK 390
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211 |  |  221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381         
                                                                                                                                                                                                                                             213  |                                                                                                                                                                              
                                                                                                                                                                                                                                                216

Chain B from PDB  Type:PROTEIN  Length:380
 aligned with MGP_BACFN | Q5LH68 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:389
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381         
            MGP_BACFN     2 SLFNDKVAKLLAGHEALLMRKNEPVEEGNGVITRYRYPVLTAAHTPVFWRYDLNEETNPFLMERIGMNATLNAGAIKWDGKYLMLVRVEGADRKSFFAVAESPNGIDNFRFWEYPVTLPEDVVPATNVYDMRLTAHEDGWIYGIFCAERHDDNAPIGDLSSATATAGIARTKDLKNWERLPDLKTKSQQRNVVLHPEFVDGKYALYTRPQDGFIDTGSGGGIGWALIDDITHAEVGEEKIIDKRYYHTIKEVKNGEGPHPIKTPQGWLHLAHGVRNCAAGLRYVLYMYMTSLDDPTRLIASPAGYFMAPVGEERIGDVSNVLFSNGWIADDDGKVFIYYASSDTRMHVATSTIERLVDYCLHTPQDGFSSSASVEILKNLIERNLRLMK 390
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhh...............eeeeeeeeeeee..eeeeeeeeee....eeeeeeee.......ee...............eeeeeeeee.....eeeeeeeeee...........eeeeeeeeee......ee........ee...ee........eeeee.ee---------.eeeeeee.hhhhh.....eeeee.........eeee....eee..eeeeeeeeeeee..eeeeeeeeeee.......eee.........hhhhhh......eeeeeeee....eeeeeeee...eeeeeeeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wau B   2 SLFNDKVAKLLAGHEALLMRKNEPVEEGNGVITRYRYPVLTAAHTPVFWRYDLNEETNPFLMERIGMNATLNAGAIKWDGKYLMLVRVEGADRKSFFAVAESPNGIDNFRFWEYPVTLPEDVVPATNVYDMRLTAHEDGWIYGIFCAERHDDNAPIGDLSSATATAGIARTKDLKNWERLPDLKTKSQQRNVVLHPEFVDGKYALYTRPQ---------GGIGWALIDDITHAEVGEEKIIDKRYYHTIKEVKNGEGPHPIKTPQGWLHLAHGVRNCAAGLRYVLYMYMTSLDDPTRLIASPAGYFMAPVGEERIGDVSNVLFSNGWIADDDGKVFIYYASSDTRMHVATSTIERLVDYCLHTPQDGFSSSASVEILKNLIERNLRLMK 390
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381         
                                                                                                                                                                                                                                           211       221

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 3WAU)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (MGP_BACFN | Q5LH68)

molecular function
	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).
	GO:0016758	transferase activity, transferring hexosyl groups	Catalysis of the transfer of a hexosyl 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:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.

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
		M1P	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MPD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ 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 ]

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

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
	3wau
		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
	MGP_BACFN \| Q5LH68
		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)
	2.4.1.281
		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
	MGP_BACFN \| Q5LH68
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	MGP_BACFN \| Q5LH68	:	3was 3wat 4kmi

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

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