3EPJ - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTALLOGRAPHIC SNAPSHOTS OF EUKARYOTIC DIMETHYLALLYLTRANSFERASE ACTING ON TRNA: INSIGHT INTO TRNA RECOGNITION AND REACTION MECHANISM

Authors :   R. H. Huang, C. Zhou

Date :   29 Sep 08 (Deposition) - 04 Nov 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym. Unit : A,B,E,F
Biol. Unit 1: A,B,E,F  (1x)
Biol. Unit 2: A,E  (1x)
Biol. Unit 3: B,F  (1x)

Keywords :   Transferase, Alternative Initiation, Atp-Binding, Cytoplasm, Mitochondrion, Nucleotide-Binding, Nucleus, Trna Processing, Transferase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Zhou, R. H. Huang
Crystallographic Snapshots Of Eukaryotic Dimethylallyltransferase Acting On Trna: Insight Into Trna Recognition And Reaction Mechanism.
Proc. Natl. Acad. Sci. Usa V. 105 16142 2008
PubMed-ID: 18852462 | Reference-DOI: 10.1073/PNAS.0805680105
(for further references see the PDB file header)

Molecule 1 - TRNA ISOPENTENYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.5.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PLM-1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 13-421
	Gene	:	MOD5
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

Molecule 2 - TRNA
	Chains	:	E, F
	Engineered	:	YES
	Other Details	:	RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	E	F
Biological Unit 1 (1x)	:	A	B	E	F
Biological Unit 2 (1x)	:	A		E
Biological Unit 3 (1x)	:		B		F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 18)

No.	Name	Count	Type	Full Name
1	MG	16	Ligand/Ion	MAGNESIUM ION
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:375 , CYS A:378 , HIS A:397 , HIS A:403	BINDING SITE FOR RESIDUE ZN A 1
02	AC2	SOFTWARE	LYS A:298	BINDING SITE FOR RESIDUE MG A 3
03	AC3	SOFTWARE	HOH A:431	BINDING SITE FOR RESIDUE MG A 5
04	AC4	SOFTWARE	G E:12	BINDING SITE FOR RESIDUE MG E 72
05	AC5	SOFTWARE	G E:15	BINDING SITE FOR RESIDUE MG E 74
06	AC6	SOFTWARE	C E:23	BINDING SITE FOR RESIDUE MG E 75
07	AC7	SOFTWARE	A E:36 , A E:37	BINDING SITE FOR RESIDUE MG E 76
08	AC8	SOFTWARE	HOH E:116 , HOH E:124	BINDING SITE FOR RESIDUE MG E 77
09	AC9	SOFTWARE	G E:53	BINDING SITE FOR RESIDUE MG E 78
10	BC1	SOFTWARE	CYS B:375 , CYS B:378 , HIS B:397 , HIS B:403	BINDING SITE FOR RESIDUE ZN B 1
11	BC2	SOFTWARE	ASP B:78 , TRP B:79 , HOH B:481	BINDING SITE FOR RESIDUE MG B 4
12	BC3	SOFTWARE	HOH F:81	BINDING SITE FOR RESIDUE MG B 7
13	BC4	SOFTWARE	G F:53	BINDING SITE FOR RESIDUE MG F 72
14	BC5	SOFTWARE	G F:27 , HOH F:80	BINDING SITE FOR RESIDUE MG F 73
15	BC6	SOFTWARE	A F:36 , A F:37 , HOH F:101 , HOH F:102	BINDING SITE FOR RESIDUE MG F 74
16	BC7	SOFTWARE	GLN B:173 , C F:35	BINDING SITE FOR RESIDUE MG F 75

(no "SS Bond" information available for 3EPJ)

(no "Cis Peptide Bond" information available for 3EPJ)

(no "SAP(SNP)/Variant" information available for 3EPJ)

(no "PROSITE Motif" information available for 3EPJ)

(no "Exon" information available for 3EPJ)

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:402
 aligned with MOD5_YEAST | P07884 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:409
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412         
           MOD5_YEAST    13 SKKVIVIAGTTGVGKSQLSIQLAQKFNGEVINSDSMQVYKDIPIITNKHPLQEREGIPHHVMNHVDWSEEYYSHRFETECMNAIEDIHRRGKIPIVVGGTHYYLQTLFNKRVDTKSSERKLTRKQLDILESTDPDVIYNTLVKCDPDIATKYHPNDYRRVQRMLEIYYKTGKKPSETFNEQKITLKFDTLFLWLYSKPEPLFQRLDDRVDDMLERGALQEIKQLYEYYSQNKFTPEQCENGVWQVIGFKEFLPWLTGKTDDNTVKLEDCIERMKTRTRQYAKRQVKWIKKMLIPDIKGDIYLLDATDLSQWDTNASQRAIAISNDFISNRPIKQERAPKALEELLSKGETTMKKLDDWTHYTCNVCRNADGKNVVAIGEKYWKIHLGSRRHKSNLKRNTRQADFEKWKI 421
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhheeeee.........hhhhhh..hhhhh....ee...........hhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhh............hhhhhhhhh....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhh.......eeeeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhh.hhhhhh...........-------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh.....eeeeeeee.....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3epj A  13 SKKVIVIAGTTGVGKSQLSIQLAQKFNGEVINSDSMQVYKDIPIITNKHPLQEREGIPHHVMNHVDWSEEYYSHRFETECMNAIEDIHRRGKIPIVVGGTHYYLQTLFNKRVDTKSSERKLTRKQLDILESTDPDVIYNTLVKCDPDIATKYHPNDYRRVQRMLEIYYKTGKKPSETFNEQKITLKFDTLFLWLYSKPEPLFQRLDDRVDDMLERGALQEIKQLYEYYSQNKFTPEQCENGVWQVIGFKEFLPWLT-------VKLEDCIERMKTRTRQYAKRQVKWIKKMLIPDIKGDIYLLDATDLSQWDTNASQRAIAISNDFISNRPIKQERAPKALEELLSKGETTMKKLDDWTHYTCNVCRNADGKNVVAIGEKYWKIHLGSRRHKSNLKRNTRQADFEKWKI 421
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262     |   -   |   282       292       302       312       322       332       342       352       362       372       382       392       402       412         
                                                                                                                                                                                                                                                                                         268     276

Chain B from PDB  Type:PROTEIN  Length:402
 aligned with MOD5_YEAST | P07884 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:409
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412         
           MOD5_YEAST    13 SKKVIVIAGTTGVGKSQLSIQLAQKFNGEVINSDSMQVYKDIPIITNKHPLQEREGIPHHVMNHVDWSEEYYSHRFETECMNAIEDIHRRGKIPIVVGGTHYYLQTLFNKRVDTKSSERKLTRKQLDILESTDPDVIYNTLVKCDPDIATKYHPNDYRRVQRMLEIYYKTGKKPSETFNEQKITLKFDTLFLWLYSKPEPLFQRLDDRVDDMLERGALQEIKQLYEYYSQNKFTPEQCENGVWQVIGFKEFLPWLTGKTDDNTVKLEDCIERMKTRTRQYAKRQVKWIKKMLIPDIKGDIYLLDATDLSQWDTNASQRAIAISNDFISNRPIKQERAPKALEELLSKGETTMKKLDDWTHYTCNVCRNADGKNVVAIGEKYWKIHLGSRRHKSNLKRNTRQADFEKWKI 421
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhheeeee.........hhhhhh..hhhhh....ee...........hhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhh............hhhhhhhhh....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhh.......eeeeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhh.hhhhhh...........-------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhh.........hhhhhhhhh.............eeeeeeee.....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3epj B  13 SKKVIVIAGTTGVGKSQLSIQLAQKFNGEVINSDSMQVYKDIPIITNKHPLQEREGIPHHVMNHVDWSEEYYSHRFETECMNAIEDIHRRGKIPIVVGGTHYYLQTLFNKRVDTKSSERKLTRKQLDILESTDPDVIYNTLVKCDPDIATKYHPNDYRRVQRMLEIYYKTGKKPSETFNEQKITLKFDTLFLWLYSKPEPLFQRLDDRVDDMLERGALQEIKQLYEYYSQNKFTPEQCENGVWQVIGFKEFLPWLT-------VKLEDCIERMKTRTRQYAKRQVKWIKKMLIPDIKGDIYLLDATDLSQWDTNASQRAIAISNDFISNRPIKQERAPKALEELLSKGETTMKKLDDWTHYTCNVCRNADGKNVVAIGEKYWKIHLGSRRHKSNLKRNTRQADFEKWKI 421
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262     |   -   |   282       292       302       312       322       332       342       352       362       372       382       392       402       412         
                                                                                                                                                                                                                                                                                         268     276

Chain E from PDB  Type:RNA  Length:69
                                                                                                     
                 3epj E   2 CUCGUAUGGCGCAGUGGUAGCGCAGCAGAUUGCAAAUCUGUUGGUCCUUAGUUCGAUCCUGAGUGCGAG  71
                                    11    ||  22        32        42        52        62         
                                         16|                                                     
                                          18

Chain F from PDB  Type:RNA  Length:69
                                                                                                     
                 3epj F   2 CUCGUAUGGCGCAGUGGUAGCGCAGCAGAUUGCAAAUCUGUUGGUCCUUAGUUCGAUCCUGAGUGCGAG  71
                                    11    ||  22        32        42        52        62         
                                         16|                                                     
                                          18

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 '\|'

(no "SCOP Domain" information available for 3EPJ)

(no "CATH Domain" information available for 3EPJ)

(no "Pfam Domain" information available for 3EPJ)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MOD5_YEAST | P07884)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
	GO:0052381	tRNA dimethylallyltransferase activity	Catalysis of the reaction: dimethylallyl diphosphate + tRNA = diphosphate + tRNA containing 6-dimethylallyladenosine.
	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.
biological process
	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.
	GO:0061587	transfer RNA gene-mediated silencing	The chromatin silencing that results in the inhibition of RNA polymerase II-transcribed genes located in the vicinity of tRNA genes.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 18)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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