1Y5V - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   TRNA-GUANINE TRANSGLYCOSYLASE (TGT) IN COMPLEX WITH 6-AMINO-4-(2-PHENYLETHYL)-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE

Authors :   B. Stengl, E. A. Meyer, A. Heine, R. Brenk, F. Diederich, G. Klebe

Date :   03 Dec 04 (Deposition) - 13 Dec 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.58

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

Keywords :   Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Stengl, E. A. Meyer, A. Heine, R. Brenk, F. Diederich, G. Klebe
Crystal Structures Of Trna-Guanine Transglycosylase (Tgt) I Complex With Novel And Potent Inhibitors Unravel Pronounced Induced-Fit Adaptations And Suggest Dimer Formation Upon Substrate Binding
J. Mol. Biol. V. 370 492 2007
PubMed-ID: 17524419 | Reference-DOI: 10.1016/J.JMB.2007.04.008
(for further references see the PDB file header)

Molecule 1 - QUEUINE TRNA-RIBOSYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.4.2.29
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET9D
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TGT
	Organism Scientific	:	ZYMOMONAS MOBILIS
	Organism Taxid	:	542
	Synonym	:	TRNA-GUANINE TRANSGLYCOSYLASE, GUANINE INSERTION ENZYME

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	NE8	1	Ligand/Ion	6-AMINO-4-(2-PHENYLETHYL)-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE
3	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	NE8	1	Ligand/Ion	6-AMINO-4-(2-PHENYLETHYL)-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	NE8	2	Ligand/Ion	6-AMINO-4-(2-PHENYLETHYL)-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

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	VAL A:45 , GLY A:69 , 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 , TYR A:258 , MET A:260 , GLY A:261	BINDING SITE FOR RESIDUE NE8 A 500
3	AC3	SOFTWARE	PRO A:56 , GLU A:57 , GLY A:94 , TRP A:95 , ASP A:96 , ARG A:97	BINDING SITE FOR RESIDUE GOL A 610
4	AC4	SOFTWARE	TRP A:296 , GLU A:317 , LYS A:360 , PHE A:373 , ARG A:380 , HOH A:1041 , HOH A:1262	BINDING SITE FOR RESIDUE GOL A 620

(no "SS Bond" information available for 1Y5V)

Asymmetric Unit

No.	Residues
1	Thr A:39	-	Pro A:40
2	Arg A:77	-	Pro A:78
3	Tyr A:161	-	Pro A:162
4	Val A:262	-	Gly A:263

(no "SAP(SNP)/Variant" information available for 1Y5V)

(no "PROSITE Motif" information available for 1Y5V)

(no "Exon" information available for 1Y5V)

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
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Chain A from PDB  Type:PROTEIN  Length:360
 aligned with TGT_ZYMMO | P28720 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:372
                                    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 RPRFSFSIAAREGKARTGTIEMKRGVIRTPAFMPVGTAATVKALKPETVRATGADIILGNTYHLMLRPGAERIAKLGGLHSFMGWDRPILTDSGGYQVMSLSSLTKQSEEGVTFKSHLDGSRHMLSPERSIEIQHLLGSDIVMAFDECTPYPATPSRAASSMERSMRWAKRSRDAFDSRKEQAENAALFGIQQGSVFENLRQQSADALAEIGFDGYAVGGLAVGEGQDEMFRVLDFSVPMLPDDKPHYLMGVGKPDDIVGAVERGIDMFDCVLPTRSGRNGQAFTWDGPINIRNARFSEDLTPLDSECHCAVCQKWSRAYIHHLIRAGEILGAMLMTEHNIAFYQQLMQKIRDSISEGRFSQFAQDFRARYF 382
               SCOP domains d1y5va_ A: Queosine tRNA-guanine transglycosylase                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1y5vA00 A:11-382 tRNA-guanine (tRNA-G) transglycosylase                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------TGT-1y5vA01 A:138-379                                                                                                                                                                                                                             --- Pfam domains
         Sec.struct. author ....eeeeeeee..eeeeeeee..eeeee.eee.ee........hhhhhhhh....eeehhhhhhhh.hhhhhhhh.hhhhhhh....eee........-----.eee..eee..-------.eehhhhhhhhhhhhh..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
                 1y5v A  11 RPRFSFSIAAREGKARTGTIEMKRGVIRTPAFMPVGTAATVKALKPETVRATGADIILGNTYHLMLRPGAERIAKLGGLHSFMGWDRPILTDSGGYQVM-----TKQSEEGVTFK-------HMLSPERSIEIQHLLGSDIVMAFDECTPYPATPSRAASSMERSMRWAKRSRDAFDSRKEQAENAALFGIQQGSVFENLRQQSADALAEIGFDGYAVGGLAVGEGQDEMFRVLDFSVPMLPDDKPHYLMGVGKPDDIVGAVERGIDMFDCVLPTRSGRNGQAFTWDGPINIRNARFSEDLKPLDSECHCAVCQKWSRAYIHHLIRAGEILGAMLMTEHNIAFYQQLMQKIRDSISEGRFSQFAQDFRARYF 382
                                    20        30        40        50        60        70        80        90       100        |-    |  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  
                                                                                                                            109   115       125     133

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: tRNA-guanine transglycosylase (91)

Family: tRNA-guanine transglycosylase (91)

Protein domain: Queosine tRNA-guanine transglycosylase (87)

Zymomonas mobilis [TaxId: 542] (67)

d1y5va_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: tRNA-guanine (tRNA-G) transglycosylase (61)

Zymomonas mobilis. Organism_taxid: 542. (48)

1y5vA00

A:11-382

Asymmetric Unit

Clans(

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Families(

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Organisms( (-)

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Clan: no clan defined [family: TGT] (33)

Family: TGT (33)

Zymomonas mobilis (33)

TGT-1y5vA01

A:138-379

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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NE8	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC4	[ 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 Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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 ](automatic orientation, automatically generated)
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	1y5v
		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)
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	TGT_ZYMMO \| P28720
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	2.4.2.29
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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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1q4w	CRYSTAL STRUCTURE OF TGT IN COMPLEX WITH 2,6-DIAMINO-3H- QUINAZOLIN-4-ONE
1q63	CRYSTAL STRUCTURE OF TGT IN COMPLEX WITH 2,6-DIAMINO-8-(1H- IMIDAZOL-2-YLSULFANYLMETHYL)-3H-QUINAZOLINE-4-ONE CRYSTALLIZED AT PH 5.5
1q65	CRYSTAL STRUCTURE OF TGT IN COMPLEX WITH 2,6-DIAMINO-8-(2- DIMETHYLAMINOETHYLSULFANYLMETHYL)-3H-QUINAZOLIN-4-ONE CRYSTALLIZED AT PH 5.5
1q66	CRYSTAL STRUCTURE OF TGT IN COMPLEX WITH 2-AMINO-6- AMINOMETHYL-8-PHENYLSULFANYLMETHYL-3H-QUINAZOLIN-4-ONE CRYSTALLIZED AT PH 5.5
1r5y	CRYSTAL STRUCTURE OF TGT IN COMPLEX WITH 2,6-DIAMINO-3H- QUINAZOLIN-4-ONE CRYSTALLIZED AT PH 5.5
1s38	CRYSTAL STRUCTURE OF TGT IN COMPLEX WITH 2-AMINO-8- METHYLQUINAZOLIN-4(3H)-ONE
1y5w	THE SAME PROTEIN WITH NEZ
1y5x	THE SAME PROTEIN WITH E89

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

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

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (7, 7)

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