4QVK - JenaLib

Title :   APO-CRYSTAL STRUCTURE OF PODOSPORA ANSERINA METHYLTRANSFERASE PAMTH1

Authors :   D. Kudlinzki, V. L. Linhard, D. Chatterjee, K. Saxena, S. Sreeramulu, H

Date :   15 Jul 14 (Deposition) - 27 May 15 (Release) - 15 Jul 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.97

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

Keywords :   Methylase, S-Adenosylmethionine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Chatterjee, D. Kudlinzki, V. Linhard, K. Saxena, U. Schieborr, S. L. Gande, J. P. Wurm, J. Wohnert, R. Abele, V. V. Rogov, V. Dotsch, H. D. Osiewacz, S. Sreeramulu, H. Schwalbe
Structure And Biophysical Characterization Of The S-Adenosylmethionine-Dependent O-Methyltransferase Pamth1, Putative Enzyme Accumulating During Senescence Of Podospora Anserina.
J. Biol. Chem. V. 290 16415 2015
PubMed-ID: 25979334 | Reference-DOI: 10.1074/JBC.M115.660829

Compounds

Molecule 1 - PAMTH1 METHYLTRANSFERASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET16B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MTH1
	Organism Scientific	:	PODOSPORA ANSERINA
	Organism Taxid	:	5145

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:11 , EDO B:301	BINDING SITE FOR RESIDUE EDO A 301
2	AC2	SOFTWARE	EDO A:301 , GLU B:137 , GLY B:161 , LEU B:163 , HOH B:597	BINDING SITE FOR RESIDUE EDO B 301

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

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:235
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhh....eeeee.hhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh..eeeeeeeee...hhhhh.............hhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qvk A   2 LGSILPFNEETADRVSAYCEKNSHGIPDALVEHWEWTRTRFPDADKMSSRLQGSWMIFTARDRKPKRILEIGCYSGYSALAWYEGTRDTKAEIVTLEYSPKMIAASREAFKKYGVGDRVKLIEGPAENTLKTLEGEFDLIFVDANKDGYAGYVKTILDQGLLSANGIILCDNVFARGLTIGPDCAPWLNDHVRPYWNGCGQALDKFSAGLMEDPRIDVLLLPVFDGVTQIRWKDG 236
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231

Chain B from PDB  Type:PROTEIN  Length:235
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhh....eeeee.hhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh..eeeeeeeee...hhhhh.............hhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qvk B   2 LGSILPFNEETADRVSAYCEKNSHGIPDALVEHWEWTRTRFPDADKMSSRLQGSWMIFTARDRKPKRILEIGCYSGYSALAWYEGTRDTKAEIVTLEYSPKMIAASREAFKKYGVGDRVKLIEGPAENTLKTLEGEFDLIFVDANKDGYAGYVKTILDQGLLSANGIILCDNVFARGLTIGPDCAPWLNDHVRPYWNGCGQALDKFSAGLMEDPRIDVLLLPVFDGVTQIRWKDG 236
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231

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 (5, 5)

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 ]

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

	Cis Peptide Bonds
		Asp A:235 - Gly A:236	[ RasMol ]
		Asp B:235 - Gly B:236	[ RasMol ]

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
	4qvk
		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
	Q9HGR1_PODAS \| Q9HGR1
		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
	Q9HGR1_PODAS \| Q9HGR1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description