1PXG - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE MUTATED TRNA-GUANINE TRANSGLYCOSYLASE (TGT) D280E COMPLEXED WITH PREQ1

Authors :   J. D. Kittendorf, T. Sgraja, K. Reuter, G. Klebe, G. A. Garcia

Date :   04 Jul 03 (Deposition) - 09 Sep 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

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

Reference :   J. D. Kittendorf, T. Sgraja, K. Reuter, G. Klebe, G. A. Garcia
An Essential Role For Aspartate 264 In Catalysis By Trna-Guanine Transglycosylase From Escherichia Coli.
J. Biol. Chem. V. 278 42369 2003
PubMed-ID: 12909636 | Reference-DOI: 10.1074/JBC.M304323200

Molecule 1 - QUEUINE TRNA-RIBOSYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.4.2.29
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETZM4
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TGT
	Mutation	:	YES
	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, 10)

No.	Name	Count	Type	Full Name
1	GOL	8	Ligand/Ion	GLYCEROL
2	PRF	1	Ligand/Ion	7-DEAZA-7-AMINOMETHYL-GUANINE
3	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	GOL	8	Ligand/Ion	GLYCEROL
2	PRF	1	Ligand/Ion	7-DEAZA-7-AMINOMETHYL-GUANINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 18)

No.	Name	Count	Type	Full Name
1	GOL	16	Ligand/Ion	GLYCEROL
2	PRF	2	Ligand/Ion	7-DEAZA-7-AMINOMETHYL-GUANINE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:318 , CYS A:320 , CYS A:323 , HIS A:349	BINDING SITE FOR RESIDUE ZN A 400
02	AC2	SOFTWARE	TYR A:106 , ASP A:156 , CYS A:158 , GLN A:203 , GLY A:229 , GLY A:230 , LEU A:231 , VAL A:233 , MET A:260 , HOH A:516	BINDING SITE FOR RESIDUE PRF A 401
03	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 1001
04	AC4	SOFTWARE	ARG A:11 , MET A:32 , LYS A:33 , ARG A:34 , GLY A:35 , VAL A:36 , HOH A:658 , HOH A:705 , HOH A:761	BINDING SITE FOR RESIDUE GOL A 1002
05	AC5	SOFTWARE	PHE A:16 , SER A:17 , ILE A:18 , ASP A:254 , HOH A:691 , HOH A:729	BINDING SITE FOR RESIDUE GOL A 1003
06	AC6	SOFTWARE	PRO A:78 , HIS A:333 , ARG A:336 , ALA A:337 , HOH A:640 , HOH A:743	BINDING SITE FOR RESIDUE GOL A 1004
07	AC7	SOFTWARE	GLU A:317 , LYS A:360 , PHE A:373 , ARG A:380 , HOH A:521 , HOH A:773	BINDING SITE FOR RESIDUE GOL A 1005
08	AC8	SOFTWARE	GLN A:117 , SER A:118 , ARG A:174 , PRO A:252 , ASP A:254 , LYS A:255 , HOH A:783 , HOH A:785	BINDING SITE FOR RESIDUE GOL A 1006
09	AC9	SOFTWARE	ALA A:61 , THR A:62 , CYS A:320 , ALA A:321 , GLU A:348 , HOH A:772	BINDING SITE FOR RESIDUE GOL A 1007
10	BC1	SOFTWARE	ARG A:38 , ARG A:60 , GLY A:63	BINDING SITE FOR RESIDUE GOL A 1008

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

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 1PXG)

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

(no "Exon" information available for 1PXG)

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:365
 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 d1pxga_ A: Queosine tRNA-guanine transglycosylase                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1pxgA00 A:11-383 tRNA-guanine (tRNA-G) transglycosylase                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------TGT-1pxgA01 A:138-379                                                                                                                                                                                                                             ---- Pfam domains
         Sec.struct. author ....eeeeeeee..eeeeeeee..eeeee.eee.ee........hhhhhhhh....eee.hhhhhh..hhhhhh...hhhhhhh....eee..hhhhhhhhh.........ee..........eehhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhheeeeee....hhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhh.....eee....hhhhhhhhhh....eee..--------.ee......ee..hhhhh...........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pxg A  11 RPRFSFSIAAREGKARTGTIEMKRGVIRTPAFMPVGTAATVKALKPETVRATGADIILGNTYHLMLRPGAERIAKLGGLHSFMGWDRPILTDSGGYQVMSLSSLTKQSEEGVTFKSHLDGSRHMLSPERSIEIQHLLGSDIVMAFDECTPYPATPSRAASSMERSMRWAKRSRDAFDSRKEQAENAALFGIQQGSVFENLRQQSADALAEIGFDGYAVGGLAVGEGQDEMFRVLDFSVPMLPDDKPHYLMGVGKPDDIVGAVERGIDMFECV--------GQAFTWDGPINIRNARFSEDLKPLDSECHCAVCQKWSRAYIHHLIRAGEILGAMLMTEHNIAFYQQLMQKIRDSISEGRFSQFAQDFRARYFA 383
                                    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 |       -|      300       310       320       330       340       350       360       370       380   
                                                                                                                                                                                                                                                                                                         282      291

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)

d1pxga_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

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)

1pxgA00

A:11-383

Asymmetric Unit

Clans(

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Families(

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Organisms( (-)

)

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

Family: TGT (33)

Zymomonas mobilis (33)

TGT-1pxgA01

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

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	1pxg
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(no "Related Entries Specified in the PDB File" available for 1PXG)

Description

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Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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