2VDV - JenaLib

Title :   STRUCTURE OF TRM8, M7G METHYLATION ENZYME

Authors :   N. Leulliot, M. Chaillet, D. Durand, N. Ulryck, K. Blondeau, H. Van Tilbeurgh

Date :   11 Oct 07 (Deposition) - 18 Dec 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : E,F
Biol. Unit 1: E  (1x)
Biol. Unit 2: F  (1x)
Biol. Unit 3: E,F  (1x)

Keywords :   S-Adenosyl-L-Methionine, Phosphorylation, Methyltransferase, M7G, Trna, Spout Mt, Transferase, Trna Processing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Leulliot, M. Chaillet, D. Durand, N. Ulryck, K. Blondeau, H. Van Tilbeurgh
Structure Of The Yeast Trna M7G Methylation Complex.
Structure V. 16 52 2008
PubMed-ID: 18184583 | Reference-DOI: 10.1016/J.STR.2007.10.025

Compounds

Molecule 1 - TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE
	Chains	:	E, F
	EC Number	:	2.1.1.33
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	GOLD (DE3)
	Expression System Taxid	:	562
	Expression System Vector	:	PET9
	Fragment	:	RESIDUES 47-286
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Other Details	:	46 N-TERMNIAL TRUNCATION
	Synonym	:	TRNA(M7G46)-METHYLTRANSFERASE, TRM8

Structural Features

Chains, Units

		1	2
Asymmetric Unit	:	E	F
Biological Unit 1 (1x)	:	E
Biological Unit 2 (1x)	:		F
Biological Unit 3 (1x)	:	E	F

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 2)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SAM	2	Ligand/Ion	S-ADENOSYLMETHIONINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SAM	1	Ligand/Ion	S-ADENOSYLMETHIONINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SAM	1	Ligand/Ion	S-ADENOSYLMETHIONINE

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	SAM	2	Ligand/Ion	S-ADENOSYLMETHIONINE

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY E:103 , CYS E:104 , GLY E:105 , GLU E:126 , ILE E:127 , ARG E:128 , GLY E:160 , ASN E:161 , ALA E:162 , CYS E:181 , PHE E:182 , ASP E:184 , THR E:259 , GLU E:261 , HOH E:2086 , HOH E:2087	BINDING SITE FOR RESIDUE SAM E1287
2	AC2	SOFTWARE	GLY F:103 , CYS F:104 , GLU F:126 , ILE F:127 , ARG F:128 , GLY F:160 , ASN F:161 , ALA F:162 , CYS F:181 , PHE F:182 , ASP F:184 , THR F:259 , GLU F:261 , HOH F:2116 , HOH F:2117 , HOH F:2119	BINDING SITE FOR RESIDUE SAM F1287

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (1, 2)

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YDL201W	1	YDL201W.1	IV:99562-100422	861	TRMB_YEAST	1-286	286	2	E:60-286 (gaps) F:60-286 (gaps)	228 228

Sequences/Alignments

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 E from PDB  Type:PROTEIN  Length:216
 aligned with TRMB_YEAST | Q12009 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:227
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       
          TRMB_YEAST     60 NPFSDHQLEYPVSPQDMDWSKLYPYYKNAENGQMTKKVTIADIGCGFGGLMIDLSPAFPEDLILGMEIRVQVTNYVEDRIIALRNNTASKHGFQNINVLRGNAMKFLPNFFEKGQLSKMFFCFPDPHFKQRKHKARIITNTLLSEYAYVLKEGGVVYTITDVKDLHEWMVKHLEEHPLFERLSKEWEENDECVKIMRNATEEGKKVERKKGDKFVACFTRLPTPAIL  286
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh..........hhhhhhhhh..----.....eeeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhh.-.......eeeee.....hhhhh.....eeeeeee....------......hhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: E:60-286 (gaps) UniProt: 1-286 [INCOMPLETE]                                                                                                                                                                          Transcript 1
                2vdv E   60 NPFSDHQLEYPVSPQDMDWSKLYPYYKN----QMTKKVTIADIGCGFGGLMIDLSPAFPEDLILGMEIRVQVTNYVEDRIIALRNNT-SKHGFQNINVLRGNAMKFLPNFFEKGQLSKMFFCFPDP------HKARIITNTLLSEYAYVLKEGGVVYTITDVKDLHEWMVKHLEEHPLFERLSKEWEENDECVKIMRNATEEGKKVERKKGDKFVACFTRLPTPAIL  286
                                    69        79       | -  |     99       109       119       129       139      |149       159       169       179     |   -  |    199       209       219       229       239       249       259       269       279       
                                                      87   92                                                   146 |               166B|              185    192                                                                                              
                                                                                                                  148                 168

Chain F from PDB  Type:PROTEIN  Length:216
 aligned with TRMB_YEAST | Q12009 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:227
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       
          TRMB_YEAST     60 NPFSDHQLEYPVSPQDMDWSKLYPYYKNAENGQMTKKVTIADIGCGFGGLMIDLSPAFPEDLILGMEIRVQVTNYVEDRIIALRNNTASKHGFQNINVLRGNAMKFLPNFFEKGQLSKMFFCFPDPHFKQRKHKARIITNTLLSEYAYVLKEGGVVYTITDVKDLHEWMVKHLEEHPLFERLSKEWEENDECVKIMRNATEEGKKVERKKGDKFVACFTRLPTPAIL  286
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh..........hhhhhhhhh..----.....eeeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhh.-.......eeeee.....hhhhh.....eeeeeee....------......hhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: F:60-286 (gaps) UniProt: 1-286 [INCOMPLETE]                                                                                                                                                                          Transcript 1
                2vdv F   60 NPFSDHQLEYPVSPQDMDWSKLYPYYKN----QMTKKVTIADIGCGFGGLMIDLSPAFPEDLILGMEIRVQVTNYVEDRIIALRNNT-SKHGFQNINVLRGNAMKFLPNFFEKGQLSKMFFCFPDP------HKARIITNTLLSEYAYVLKEGGVVYTITDVKDLHEWMVKHLEEHPLFERLSKEWEENDECVKIMRNATEEGKKVERKKGDKFVACFTRLPTPAIL  286
                                    69        79       | -  |     99       109       119       129       139      |149       159       169       179     |   -  |    199       209       219       229       239       249       259       269       279       
                                                      87   92                                                   146 |               166B|              185    192                                                                                              
                                                                                                                  148                 168

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 (14, 14)

Visualization

Interactive Views

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

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

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2vdv)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Still Images

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 \| Biol. Unit 2 PNG format \| Biol. Unit 3 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
	2vdv
		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
	TRMB_YEAST \| Q12009
		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)
	2.1.1.33
		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
	TRMB_YEAST \| Q12009
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description