2ZU9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE FROM PYROCOCCUS HORIKOSHII

Authors :   T. Kawamura, N. Watanabe, I. Tanaka

Date :   14 Oct 08 (Deposition) - 27 Oct 09 (Release) - 27 Oct 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Gt-A Fold, Glycosyltransferase, Gt55, Gdp, Cytoplasm, Magnesium, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Kawamura, N. Watanabe, I. Tanaka
Crystal Structure Of Mannosyl-3-Phosphoglycerate Synthase From Pyrococcus Horikoshii
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE
	Chains	:	A, B
	EC Number	:	2.4.1.217
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PH0927
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	53953
	Strain	:	OT3
	Synonym	:	MPG SYNTHASE, MPGS

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 34)

No.	Name	Count	Type	Full Name
1	CO	2	Ligand/Ion	COBALT (II) ION
2	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MSE	30	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO B:58 , MSE B:59 , LYS B:60 , GLU B:62 , VAL B:83 , ASN B:85 , GLN B:117 , GLY B:144 , LYS B:145 , ASP B:168 , ALA B:169 , ASP B:170 , TYR B:268 , HIS B:312 , LYS B:315 , CO B:395	BINDING SITE FOR RESIDUE GDP A 395
2	AC2	SOFTWARE	PRO A:58 , MSE A:59 , LYS A:60 , GLU A:62 , VAL A:83 , ASN A:85 , GLN A:117 , GLY A:144 , LYS A:145 , ASP A:168 , ALA A:169 , ASP A:170 , TYR A:268 , HIS A:312 , LYS A:315 , HIS A:319 , CO A:397	BINDING SITE FOR RESIDUE GDP A 396
3	AC3	SOFTWARE	ASP A:170 , HIS A:312 , LYS A:315 , GDP A:396	BINDING SITE FOR RESIDUE CO A 397
4	AC4	SOFTWARE	GDP A:395 , ASP B:170 , HIS B:312 , HOH B:410	BINDING SITE FOR RESIDUE CO B 395

(no "SS Bond" information available for 2ZU9)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:90	-	Pro A:91
2	Gly B:90	-	Pro B:91

(no "SAP(SNP)/Variant" information available for 2ZU9)

(no "PROSITE Motif" information available for 2ZU9)

(no "Exon" information available for 2ZU9)

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:369
 aligned with MPGS_PYRHO | O58689 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:394
                                    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    
           MPGS_PYRHO     1 MLLEAPVYKEIFGAVTIHEVQKVIKMDTETEEVPIYTISNIPREKIYDLLGKMAVIVPMKNEKLHLVDGVLKAIPHKCPIIIVSNSKREGPNRYKLEVDLIRHFYNLTHSKIIMIHQKDPGLAKAFKEVGYTDILDENGMIRSGKGEGMLVGLLLAKAIGAEYVGFVDADNYIPGAVNEYVKDYAAGFLMSESEYTMVRLHWRHKPKVTKGTLYFKKWGRVSEITNHYLNLLVSEHTAFETTIMVTGNAGEHAMTMKLAEILPFSTGYSIEPYEIVYILERFGKWENVEEFKDVFDQGIEIFQIETLNPHFHEDKGKEHVKEMLLLSLATIYHSKLATDNLRKRILKDLRDHGILGENEEPPKPLVMRPIKEIPIKEWMDIVEGNSETLLRFEL 394
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eeee..eeee..eeeee...--------.eee.hhhhhhhhhh.eeeeeee...hhhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh..............hhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhhh....eeeeee.-----------------hhhhhhhhhhhhhhhhhhh.............eeeehhhhh...ee...hhhhhhhhhhhhhhh....hhhhhhhhhhheeeeeee..........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.............ee......hhhhhhhhhhhhh...eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zu9 A   1 mLLEAPVYKEIFGAVTIHEVQKVIKmDT--------TISNIPREKIYDLLGKmAVIVPmKNEKLHLVDGVLKAIPHKCPIIIVSNSKREGPNRYKLEVDLIRHFYNLTHSKIImIHQKDPGLAKAFKEVGYTDILDENGmIRSGKGEGmLVGLLLAKAIGAEYVGFVDADNYIPGAVNEYVKDYAAGFLmSESEYTmVRLHW-----------------RVSEITNHYLNLLVSEHTAFETTImVTGNAGEHAmTmKLAEILPFSTGYSIEPYEIVYILERFGKWENVEEFKDVFDQGIEIFQIETLNPHFHEDKGKEHVKEmLLLSLATIYHSKLATDNLRKRILKDLRDHGILGENEEPPKPLVmRPIKEIPIKEWmDIVEGNSETLLRFEL 394
                            |       10        20     | | -      | 40        50  |     60        70        80        90       100       110   |   120       130       140       150       160       170       180       190      |200 |       -       220       230       240   |   250   | | 260       270       280       290       300       310       320  |    330       340       350       360      |370       380       390    
                            |                       26-MSE     37              53-MSE |                                                    114-MSE                   140-MSE  149-MSE                                  190-MSE  |  202               220                     244-MSE   254-MSE                                                              323-MSE                                     367-MSE     379-MSE           
                            1-MSE                     28                             59-MSE                                                                                                                                   197-MSE                                                    256-MSE

Chain B from PDB  Type:PROTEIN  Length:359
 aligned with MPGS_PYRHO | O58689 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:394
                                    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    
           MPGS_PYRHO     1 MLLEAPVYKEIFGAVTIHEVQKVIKMDTETEEVPIYTISNIPREKIYDLLGKMAVIVPMKNEKLHLVDGVLKAIPHKCPIIIVSNSKREGPNRYKLEVDLIRHFYNLTHSKIIMIHQKDPGLAKAFKEVGYTDILDENGMIRSGKGEGMLVGLLLAKAIGAEYVGFVDADNYIPGAVNEYVKDYAAGFLMSESEYTMVRLHWRHKPKVTKGTLYFKKWGRVSEITNHYLNLLVSEHTAFETTIMVTGNAGEHAMTMKLAEILPFSTGYSIEPYEIVYILERFGKWENVEEFKDVFDQGIEIFQIETLNPHFHEDKGKEHVKEMLLLSLATIYHSKLATDNLRKRILKDLRDHGILGENEEPPKPLVMRPIKEIPIKEWMDIVEGNSETLLRFEL 394
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Osmo_MPGsynth-2zu9B01 B:3-        383                                                                                                                                                                                                                                                                                                                                                        ----------- Pfam domains (1)
           Pfam domains (2) --Osmo_MPGsynth-2zu9B02 B:3-        383                                                                                                                                                                                                                                                                                                                                                        ----------- Pfam domains (2)
         Sec.struct. author .eee....eeee..eeee..eeeee...--------.eee.hhhhhhhhhh.eeeeeee...hhhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh..............hhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhhh....eeeeee.------------------hhhhhhhhhhhhhhhhhh.............eeeehhhhh........hhhhhhhhhhhhhhh...hhhhhhhhhhhheeeeeee..........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh---------...............hhhhhhhhhhhhh...eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zu9 B   1 mLLEAPVYKEIFGAVTIHEVQKVIKmDT--------TISNIPREKIYDLLGKmAVIVPmKNEKLHLVDGVLKAIPHKCPIIIVSNSKREGPNRYKLEVDLIRHFYNLTHSKIImIHQKDPGLAKAFKEVGYTDILDENGmIRSGKGEGmLVGLLLAKAIGAEYVGFVDADNYIPGAVNEYVKDYAAGFLmSESEYTmVRLHW------------------VSEITNHYLNLLVSEHTAFETTImVTGNAGEHAmTmKLAEILPFSTGYSIEPYEIVYILERFGKWENVEEFKDVFDQGIEIFQIETLNPHFHEDKGKEHVKEmLLLSLATIYHSKLATDNLRKRILKDL---------EEPPKPLVmRPIKEIPIKEWmDIVEGNSETLLRFEL 394
                            |       10        20     | | -      | 40        50  |     60        70        80        90       100       110   |   120       130       140       150       160       170       180       190      |200 |       -         -|      230       240   |   250   | | 260       270       280       290       300       310       320  |    330       340        |-       360      |370       380       390    
                            1-MSE                   26-MSE     37              53-MSE |                                                    114-MSE                   140-MSE  149-MSE                                  190-MSE  |  202                221                    244-MSE   254-MSE                                                              323-MSE                   349       359     367-MSE     379-MSE           
                                                      28                             59-MSE                                                                                                                                   197-MSE                                                    256-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 2ZU9)

(no "CATH Domain" information available for 2ZU9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (MPGS_PYRHO | O58689)

molecular function
	GO:0050504	mannosyl-3-phosphoglycerate synthase activity	Catalysis of the reaction: 3-phospho-D-glycerate + GDP-alpha-D-mannose = 2-(alpha-D-mannosyl)-3-phosphoglycerate + GDP + H(+).
	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:0051479	mannosylglycerate biosynthetic process	The chemical reactions and pathways resulting in the formation of mannosylglycerate, a very common compatible solute in thermophilic and hyperthermophilic organisms.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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
		CO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GDP	[ 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
		Gly A:90 - Pro A:91	[ RasMol ]
		Gly B:90 - Pro B:91	[ 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
	2zu9
		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
	MPGS_PYRHO \| O58689
		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)
	2.4.1.217
		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
	MPGS_PYRHO \| O58689
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	MPGS_PYRHO \| O58689	:	2zu7 2zu8

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 34)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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 (1, 2)

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