4XBO - JenaLib

Title :   CRYSTAL STRUCTURE OF FULL LENGTH E.COLI TRMJ IN COMPLEX WITH SAH

Authors :   R. J. Liu, T. Long, M. Zhou, E. D. Wang

Date :   17 Dec 14 (Deposition) - 23 Dec 15 (Release) - 23 Dec 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Spout, Trna, Methyltransferase, Rna Modification, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. J. Liu, T. Long, M. Zhou, X. L. Zhou, E. D. Wang
Trna Recognition By A Bacterial Trna Xm32 Modification Enzyme From The Spout Methyltransferase Superfamily
Nucleic Acids Res. V. 43 7489 2015
PubMed-ID: 26202969 | Reference-DOI: 10.1093/NAR/GKV745

Compounds

Molecule 1 - TRNA (CYTIDINE/URIDINE-2'-O-)-METHYLTRANSFERASE TRMJ
	Chains	:	A, B
	EC Number	:	2.1.1.200
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TRMJ, YFHQ, B2532, JW2516
	Organism Scientific	:	ESCHERICHIA COLI K12
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	TRNA (CYTIDINE(32)/URIDINE(32)-2'-O)-METHYLTRANSFERASE, TRNA CM32/UM32 METHYLTRANSFERASE

Structural Features

Chains, Units

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:79 , SER A:80 , ALA A:81 , PHE A:113 , GLY A:114 , ARG A:115 , GLY A:119 , VAL A:132 , ALA A:133 , ILE A:134 , SER A:141 , SER A:142 , LEU A:143 , ALA A:148 , HOH A:422	binding site for residue SAH A 301
2	AC2	SOFTWARE	THR B:79 , SER B:80 , ALA B:81 , PHE B:113 , GLY B:114 , ARG B:115 , ARG B:117 , GLY B:119 , VAL B:132 , ILE B:134 , SER B:141 , SER B:142 , LEU B:143 , LEU B:145 , ALA B:148 , HOH B:423 , HOH B:433	binding site for residue SAH B 301

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:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhh.eeeeee.....hhhhhhhhhhhhh....eeee...............hhhhhhhh.eee.hhhhhh....eeeee..........eehhhhhhhhhhhhhh...eeeee.......hhhhhh...eee...........hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xbo A   1 MLQNIRIVLVETSHTGNMGSVARAMKTMGLTNLWLVNPLVKPDSQAIALAAGASDVIGNAHIVDTLDEALAGCSLVVGTSARSRTLPWPMLDPRECGLKSVAEAANTPVALVFGRERVGLTNEELQKCHYHVAIAANPEYSSLNLAMAVQVIAYEVRMAWLATQTPYPLVDDLERFYGHLEQTLLATGFIRENHPGQVMNKLRRLFTRARPESQELNILRGILASIEQ 238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   ||  180       190       200       210       220       230        
                                                                                                                                                                                             164|                                                               
                                                                                                                                                                                              175

Chain B from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeeeee...hhhhhhhhhhhhhhhh...eeee.........hhhhhhh.eee.hhhhhhh...eeeee..........eehhhhhhhhhhhhhh...eeeee.......hhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xbo B   1 MLQNIRIVLVETSHTGNMGSVARAMKTMGLTNLWLVNPLVKPAAGASDVIGNAHIVDTLDEALAGCSLVVGTSARSRTLPWPMLDPRECGLKSVAEAANTPVALVFGRERVGLTNEELQKCHYHVAIAANPEYSSLNLAMAVQVIAYEVRMAWLATQENETPYPLVDDLERFYGHLEQTLLATGFIRENHPGQVMNKLRRLFTRARPESQELNILRGILASIEQQN 240
                                    10        20        30        40 ||     57        67        77        87        97       107       117       127       137       147       157       174       184       194       204       214       224       234      
                                                                    42|                                                                                                                 166|                                                                  
                                                                     50                                                                                                                  174

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 (12, 12)

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

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

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4xbo)

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
	4xbo
		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
	TRMJ_ECOLI \| P0AE01
		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)
	2.1.1.200
		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
	TRMJ_ECOLI \| P0AE01
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description