2PWV - JenaLib

Title :   TRNA GUANINE TRANSGLYCOSYLASE E235Q MUTANT IN COMPLEX WITH PREQ0

Authors :   N. Tidten, B. Stengl, A. Heine, K. Reuter, G. Klebe

Date :   13 May 07 (Deposition) - 30 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Tgt, E235Q Mutant, Preq0, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Tidten, B. Stengl, A. Heine, G. A. Garcia, G. Klebe, K. Reuter
Glutamate Versus Glutamine Exchange Swaps Substrate Selectivity In Trna-Guanine Transglycosylase: Insight Into The Regulation Of Substrate Selectivity By Kinetic And Crystallographic Studies.
J. Mol. Biol. V. 374 764 2007
PubMed-ID: 17949745 | Reference-DOI: 10.1016/J.JMB.2007.09.062

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:318 , CYS A:320 , CYS A:323 , HIS A:349	BINDING SITE FOR RESIDUE ZN A 400
2	AC2	SOFTWARE	ASP A:102 , SER A:103 , TYR A:106 , ASP A:156 , CYS A:158 , ILE A:201 , GLN A:203 , GLY A:229 , GLY A:230 , LEU A:231 , ALA A:232 , MET A:260 , GOL A:703	BINDING SITE FOR RESIDUE PQ0 A 500
3	AC3	SOFTWARE	GLU A:57 , GLY A:94 , TRP A:95 , ASP A:96 , ARG A:97	BINDING SITE FOR RESIDUE GOL A 600
4	AC4	SOFTWARE	VAL A:45 , ASN A:70 , GLN A:107 , ASP A:280 , PQ0 A:500	BINDING SITE FOR RESIDUE GOL A 703
5	AC5	SOFTWARE	HIS A:145 , GLY A:148 , SER A:149 , GLU A:191 , GLN A:192 , HOH A:775 , HOH A:789 , HOH A:819	BINDING SITE FOR RESIDUE GOL A 705
6	AC6	SOFTWARE	TRP A:296 , GLU A:317 , LYS A:360 , PHE A:373 , ARG A:380	BINDING SITE FOR RESIDUE GOL A 706
7	AC7	SOFTWARE	GLU A:22 , GLY A:23 , LYS A:24 , ALA A:25 , GLU A:273 , PHE A:370	BINDING SITE FOR RESIDUE GOL A 716
8	AC8	SOFTWARE	PRO A:249 , LEU A:251 , PRO A:252 , ASP A:253 , HOH A:900	BINDING SITE FOR RESIDUE GOL A 717

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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 A from PDB  Type:PROTEIN  Length:361
 aligned with TGT_ZYMMO | P28720 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:373
                                    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   
            TGT_ZYMMO    11 RPRFSFSIAAREGKARTGTIEMKRGVIRTPAFMPVGTAATVKALKPETVRATGADIILGNTYHLMLRPGAERIAKLGGLHSFMGWDRPILTDSGGYQVMSLSSLTKQSEEGVTFKSHLDGSRHMLSPERSIEIQHLLGSDIVMAFDECTPYPATPSRAASSMERSMRWAKRSRDAFDSRKEQAENAALFGIQQGSVFENLRQQSADALAEIGFDGYAVGGLAVGEGQDEMFRVLDFSVPMLPDDKPHYLMGVGKPDDIVGAVERGIDMFDCVLPTRSGRNGQAFTWDGPINIRNARFSEDLTPLDSECHCAVCQKWSRAYIHHLIRAGEILGAMLMTEHNIAFYQQLMQKIRDSISEGRFSQFAQDFRARYFA 383
               SCOP domains d2pwva_ A: Queosine tRNA-guanine transglycosylase                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2pwvA00 A:11-383 tRNA-guanine (tRNA-G) transglycosylase                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------TGT-2pwvA01 A:138-379                                                                                                                                                                                                                             ---- Pfam domains
         Sec.struct. author ....eeeeeeee..eeeeeeee..eeeee.eee.ee........hhhhhhhh....eeeehhhhhhh.hhhhhhhh.hhhhhhh....eeee.hhhhhhhh----..........--------..hhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee....hhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhh.....eee....hhhhhhhhhh....eee.hhhhhhhhh.ee......ee..hhhhh...........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pwv A  11 RPRFSFSIAAREGKARTGTIEMKRGVIRTPAFMPVGTAATVKALKPETVRATGADIILGNTYHLMLRPGAERIAKLGGLHSFMGWDRPILTDSGGYQVMSL----KQSEEGVTFK--------MLSPERSIEIQHLLGSDIVMAFDECTPYPATPSRAASSMERSMRWAKRSRDAFDSRKEQAENAALFGIQQGSVFENLRQQSADALAEIGFDGYAVGGLAVGQGQDEMFRVLDFSVPMLPDDKPHYLMGVGKPDDIVGAVERGIDMFDCVLPTRSGRNGQAFTWDGPINIRNARFSEDLKPLDSECHCAVCQKWSRAYIHHLIRAGEILGAMLMTEHNIAFYQQLMQKIRDSISEGRFSQFAQDFRARYFA 383
                                    20        30        40        50        60        70        80        90       100       110|    | 120    |    -   |   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   
                                                                                                                              111  116      125      134

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 (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A (TGT_ZYMMO | P28720)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008479	queuine tRNA-ribosyltransferase activity	Catalysis of the reaction: tRNA guanine + queuine = tRNA queuine + guanine.
	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:0008616	queuosine biosynthetic process	The chemical reactions and pathways resulting in the formation of queuosines, any of a series of nucleosides found in tRNA and having an additional pentenyl ring added via an NH group to the methyl group of 7-methylguanosine. The pentenyl ring may carry other substituents.
	GO:0006400	tRNA modification	The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.

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
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PQ0	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ 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 ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Arg A:77 - Pro A:78	[ RasMol ]
		Thr A:39 - Pro A:40	[ RasMol ]
		Tyr A:161 - Pro A:162	[ RasMol ]
		Val A:262 - Gly A:263	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2pwv
		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
	TGT_ZYMMO \| P28720
		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)
	2.4.2.29
		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

Description