5GWX - JenaLib

Title :   CRYSTAL STRUCTURE OF GLYCINE SARCOSINE N-METHYLTRANSFERASE FROM METHANOHALOPHILUS PORTUCALENSIS IN COMPLEX WITH S-ADENOSYLMETHIONINE AND SARCOSINE

Authors :   Y. R. Lee, T. S. Lin, S. J. Lai, M. S. Liu, M. C. Lai, N. L. Chan

Date :   14 Sep 16 (Deposition) - 23 Nov 16 (Release) - 18 Jan 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.21

Chains :   Asym./Biol. Unit : A

Keywords :   S-Adenosylmethionine-Dependent Methyltransferases, Sam, Adomet-Mtase, Class I Monomethylation, Glycine, Sarcosine Rate-Limiting Enzyme, Betaine Biosynthesis Betaine-Mediated Feedback Inhibition, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. R. Lee, T. S. Lin, S. J. Lai, M. S. Liu, M. C. Lai, N. L. Chan
Structural Analysis Of Glycine Sarcosine N-Methyltransferas From Methanohalophilus Portucalensis Reveals Mechanistic Insights Into The Regulation Of Methyltransferase Activity.
Sci Rep V. 6 38071 2016
PubMed-ID: 27934872 | Reference-DOI: 10.1038/SREP38071

Compounds

Molecule 1 - GLYCINE SARCOSINE N-METHYLTRANSFERASE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Gene	:	GSMT
	Organism Scientific	:	METHANOHALOPHILUS PORTUCALENSIS FDF-1
	Organism Taxid	:	523843

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:43 , ALA A:67 , THR A:68 , GLY A:69 , ASN A:73 , ASP A:88 , GLY A:89 , MET A:93 , ALA A:113 , TRP A:115 , LEU A:132 , GLY A:133 , SER A:135 , SAR A:302 , HOH A:416 , HOH A:479 , HOH A:496	binding site for residue SAM A 301
2	AC2	SOFTWARE	GLY A:133 , ASN A:134 , HIS A:138 , ARG A:167 , TYR A:206 , SAM A:301	binding site for residue SAR A 302
3	AC3	SOFTWARE	TRP A:40 , ASN A:100 , HIS A:104	binding site for residue EDO A 303
4	AC4	SOFTWARE	ARG A:167 , ASN A:168 , ILE A:172 , ASP A:254	binding site for residue EDO A 304
5	AC5	SOFTWARE	GLU A:47 , ILE A:51 , ILE A:52 , ASN A:73 , ARG A:76 , HOH A:466	binding site for residue EDO A 305
6	AC6	SOFTWARE	TRP A:40 , ALA A:44 , ARG A:76 , GLN A:79 , HIS A:104	binding site for residue EDO A 306

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

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:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh...eeee.....hhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhh.....eee.hhhhhhhh....eeeeee...hhhhh.hhhhhhhhhhhhhhheeeeeeeeeeeehhhhhhhhhhhhh..eee....eeeeeeeee..eeeeeeee....eeeeee...hhhhhhhhhhhh...eeeeeee...........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gwx A  15 EVRESDHYEEEYVLGFVDKWDELIDWESRAESEGDTIINILKERGVKKVLDVATGTGFNSVRLLQAGFDVVSADGSAEMLVKAFDNARDHGYLMRTVQADWRWMNKDIHDKFDAIVCLGNSFTHLFDEGDRRKALAEFYALLKHDGVLLLDQRNYDAILDDGYSSKHAHYYCGDTVSVYPEHVDEGLARFKYEFSDGSVYNLNMFPLRKDYTRQLLHEVGFQEINTLGDFKETYKEDEPDFFLHVAEKN 263
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

Visualization

Interactive Views

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
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SAM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SAR	[ 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 ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5gwx)

Still Images

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)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	5gwx
		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
	F6KV61_9EURY \| F6KV61
		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)
	(no 'Enzyme Classificator' available)
		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

Analysis Tools

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
	F6KV61_9EURY \| F6KV61
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description