1Q63 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TGT IN COMPLEX WITH 2,6-DIAMINO-8-(1H-IMIDAZOL-2-YLSULFANYLMETHYL)-3H-QUINAZOLINE-4-ONE CRYSTALLIZED AT PH 5.5

Authors :   R. Brenk, E. Meyer, K. Reuter, M. T. Stubbs, G. A. Garcia, G. Klebe

Date :   12 Aug 03 (Deposition) - 13 Apr 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

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

Reference :   R. Brenk, E. Meyer, K. Reuter, M. T. Stubbs, G. A. Garcia, F. Diederich, G. Klebe
Crystallographic Study Of Inhibitors Of Trna-Guanine Transglycosylase Suggests A New Structure-Based Pharmacophore For Virtual Screening.
J. Mol. Biol. V. 338 55 2004
PubMed-ID: 15050823 | Reference-DOI: 10.1016/J.JMB.2004.02.019

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, TGT

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	AIQ	1	Ligand/Ion	2,6-DIAMINO-8-(1H-IMIDAZOL-2-YLSULFANYLMETHYL)-3H-QUINAZOLINE-4-ONE
2	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	AIQ	1	Ligand/Ion	2,6-DIAMINO-8-(1H-IMIDAZOL-2-YLSULFANYLMETHYL)-3H-QUINAZOLINE-4-ONE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	AIQ	2	Ligand/Ion	2,6-DIAMINO-8-(1H-IMIDAZOL-2-YLSULFANYLMETHYL)-3H-QUINAZOLINE-4-ONE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

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 , ASP A:156 , CYS A:158 , ILE A:201 , GLN A:203 , GLY A:229 , GLY A:230 , LEU A:231 , MET A:260 , GLY A:261 , ASP A:280	BINDING SITE FOR RESIDUE AIQ A 900

(no "SS Bond" information available for 1Q63)

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

(no "SAP(SNP)/Variant" information available for 1Q63)

(no "PROSITE Motif" information available for 1Q63)

(no "Exon" information available for 1Q63)

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:366
 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 d1q63a_ A: Queosine tRNA-guanine transglycosylase                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1q63A00 A:11-382 tRNA-guanine (tRNA-G) transglycosylase                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------TGT-1q63A01 A:138-379                                                                                                                                                                                                                             --- Pfam domains
         Sec.struct. author ...eeeeeeeee..eeeeeeee..eeeee.eeeeee........hhhhhhhh....eeehhhhhhhh.hhhhhhhh.hhhhhhh....eee.....hhhhhh--.eee..eeee...----.eeehhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee....hhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhh.....eee....hhhhhhhhhh....eeeehhhhhhhhhhee......ee..hhhhh...........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1q63 A  11 RPRFSFSIAAREGKARTGTIEMKRGVIRTPAFMPVGTAATVKALKPETVRATGADIILGNTYHLMLRPGAERIAKLGGLHSFMGWDRPILTDSGGYQVMSLS--TKQSEEGVTFKSH----RHMLSPERSIEIQHLLGSDIVMAFDECTPYPATPSRAASSMERSMRWAKRSRDAFDSRKEQAENAALFGIQQGSVFENLRQQSADALAEIGFDGYAVGGLAVGEGQDEMFRVLDFSVPMLPDDKPHYLMGVGKPDDIVGAVERGIDMFDCVLPTRSGRNGQAFTWDGPINIRNARFSEDLKPLDSECHCAVCQKWSRAYIHHLIRAGEILGAMLMTEHNIAFYQQLMQKIRDSISEGRFSQFAQDFRARYF 382
                                    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  
                                                                                                                               112  |         127  132                                                                                                                                                                                                                                                          
                                                                                                                                  115

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)

d1q63a_

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)

1q63A00

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-1q63A01

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.

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

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

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	1q63
		Family and Domain Information	:	ProDom \| SYSTERS
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		Orientation in Membranes	:	OPM
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	TGT_ZYMMO \| P28720
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	2.4.2.29
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		Interatomic Contacts of Structural Units	:	CSU
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1k4g	CRYSTAL STRUCTURE OF TRNA-GUANINE TRANSGLYCOSYLASE (TGT) COMPLEXED WITH 2,6-DIAMINO-8-(1H-IMIDAZOL-2- YLSULFANYLMETHYL)-3H-QUINAZOLINE-4-ONE
1pud	TRNA-GUANINE TRANSGLYCOSYLASE
1q4w	CORE STRUCTURE OF 2,6-DIAMINO-8-(1H-IMIDAZOL-2- YLSULFANYLMETHYL)-3H-QUINAZOLINE-4-ONE IN COMPLEX WITH TGT, CRYSTALLIZED AT PH 8.5
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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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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