2ZXU - JenaLib

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Title :   CRYSTAL STRUCTURE OF TRNA MODIFICATION ENZYME MIAA IN THE COMPLEX WITH TRNA(PHE) AND DMASPP

Authors :   J. Sakai, M. Yao, S. Chimnaronk, I. Tanaka

Date :   07 Jan 09 (Deposition) - 26 May 09 (Release) - 16 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)
Biol. Unit 3: A,B,C,D  (1x)

Keywords :   Protein-Rna Complex, Atp-Binding, Trna Modification Enzyme, Nucleotide-Binding, Nucleotidyltransferase, Transferase, Trna Processing, Transferase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Chimnaronk, F. Forouhar, J. Sakai, M. Yao, C. M. Tron, M. Atta, M. Fontecave, J. F. Hunt, I. Tanaka
Snapshots Of Dynamics In Synthesizing N(6)-Isopentenyladenosine At The Trna Anticodon
Biochemistry V. 48 5057 2009
PubMed-ID: 19435325 | Reference-DOI: 10.1021/BI900337D
(for further references see the PDB file header)

Molecule 1 - TRNA DELTA(2)-ISOPENTENYLPYROPHOSPHATE TRANSFERASE
	Chains	:	A, B
	Diphosphate	:	TRNA ISOPENTENYLTRANSFERASE, IPTASE, IPPT
	EC Number	:	2.5.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MINAA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K-12
	Synonym	:	MIAA, IPP TRANSFERASE, ISOPENTENYL-

Molecule 2 - TRNA(PHE)
	Chains	:	C, D
	Engineered	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Other Details	:	TRNA(PHE) WAS PREPARED BY IN VITRO TRANSCRIPTION. THIS SEQUENCE OCCURS NATURALLY IN ESCHERICHIA COLI ST.K12.
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D
Biological Unit 3 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	DST	2	Ligand/Ion	DIMETHYLALLYL S-THIOLODIPHOSPHATE
2	MG	10	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	DST	1	Ligand/Ion	DIMETHYLALLYL S-THIOLODIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	DST	1	Ligand/Ion	DIMETHYLALLYL S-THIOLODIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	DST	2	Ligand/Ion	DIMETHYLALLYL S-THIOLODIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:19 , ALA A:20 , SER A:21 , GLY A:22 , LYS A:23 , THR A:24 , GLY A:53 , THR A:54 , ARG A:217 , LEU A:278 , MG A:318 , HOH A:343 , HOH A:366 , HOH A:372 , A C:37	BINDING SITE FOR RESIDUE DST A 317
02	AC2	SOFTWARE	THR B:19 , ALA B:20 , SER B:21 , GLY B:22 , LYS B:23 , THR B:24 , THR B:54 , ALA B:55 , ARG B:217 , MG B:318 , HOH B:322 , HOH B:325 , HOH B:348	BINDING SITE FOR RESIDUE DST B 317
03	AC3	SOFTWARE	U C:16 , C C:17 , G C:19	BINDING SITE FOR RESIDUE MG C 77
04	AC4	SOFTWARE	G C:27 , HOH C:108	BINDING SITE FOR RESIDUE MG C 78
05	AC5	SOFTWARE	A C:7 , U C:8 , A C:14 , HOH C:112 , HOH C:113	BINDING SITE FOR RESIDUE MG C 79
06	AC6	SOFTWARE	G D:27 , HOH D:142	BINDING SITE FOR RESIDUE MG D 77
07	AC7	SOFTWARE	U C:59 , U C:60	BINDING SITE FOR RESIDUE MG C 80
08	AC8	SOFTWARE	A C:58 , U C:59	BINDING SITE FOR RESIDUE MG C 81
09	AC9	SOFTWARE	G C:22 , U C:45 , G C:46 , HOH C:195	BINDING SITE FOR RESIDUE MG C 82
10	BC1	SOFTWARE	U C:12	BINDING SITE FOR RESIDUE MG C 83
11	BC2	SOFTWARE	THR A:24 , DST A:317	BINDING SITE FOR RESIDUE MG A 318
12	BC3	SOFTWARE	THR B:24 , ALA B:55 , DST B:317	BINDING SITE FOR RESIDUE MG B 318

(no "SS Bond" information available for 2ZXU)

(no "Cis Peptide Bond" information available for 2ZXU)

(no "SAP(SNP)/Variant" information available for 2ZXU)

(no "PROSITE Motif" information available for 2ZXU)

(no "Exon" information available for 2ZXU)

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:306
 aligned with MIAA_ECOLI | P16384 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:306
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308      
           MIAA_ECOLI     9 LPKAIFLMGPTASGKTALAIELRKILPVELISVDSALIYKGMDIGTAKPNAEELLAAPHRLLDIRDPSQAYSAADFRRDALAEMADITAAGRIPLLVGGTMLYFKALLEGLSPLPSADPEVRARIEQQAAEQGWESLHRQLQEVDPVAAARIHPNDPQRLSRALEVFFISGKTLTELTQTSGDALPYQVHQFAIAPASRELLHQRIEQRFHQMLASGFEAEVRALFARGDLHTDLPSIRCVGYRQMWSYLEGEISYDEMVYRGVCATRQLAKRQITWLRGWEGVHWLDSEKPEQARDEVLQVVGAI 314
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhh.eeeeee................hhhhhhhh.ee...........hhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhh.........eeeeeeee..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.............hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zxu A   9 LPKAIFLMGPTASGKTALAIELRKILPVELISVDSALIYKGMDIGTAKPNAEELLAAPHRLLDIRDPSQAYSAADFRRDALAEMADITAAGRIPLLVGGTMLYFKALLEGLSPLPSADPEVRARIEQQAAEQGWESLHRQLQEVDPVAAARIHPNDPQRLSRALEVFFISGKTLTELTQTSGDALPYQVHQFAIAPASRELLHQRIEQRFHQMLASGFEAEVRALFARGDLHTDLPSIRCVGYRQMWSYLEGEISYDEMVYRGVCATRQLAKRQITWLRGWEGVHWLDSEKPEQARDEVLQVVGAI 314
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308

Chain B from PDB  Type:PROTEIN  Length:305
 aligned with MIAA_ECOLI | P16384 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:305
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306     
           MIAA_ECOLI     7 ASLPKAIFLMGPTASGKTALAIELRKILPVELISVDSALIYKGMDIGTAKPNAEELLAAPHRLLDIRDPSQAYSAADFRRDALAEMADITAAGRIPLLVGGTMLYFKALLEGLSPLPSADPEVRARIEQQAAEQGWESLHRQLQEVDPVAAARIHPNDPQRLSRALEVFFISGKTLTELTQTSGDALPYQVHQFAIAPASRELLHQRIEQRFHQMLASGFEAEVRALFARGDLHTDLPSIRCVGYRQMWSYLEGEISYDEMVYRGVCATRQLAKRQITWLRGWEGVHWLDSEKPEQARDEVLQVV 311
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------IPPT-2zxuB01 B:44-298                                                                                                                                                                                                                                          ------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------IPPT-2zxuB02 B:44-298                                                                                                                                                                                                                                          ------------- Pfam domains (2)
         Sec.struct. author ....eeeeee.....hhhhhhhhhhhhh.eeeeee................hhhhhhhh.ee...........hhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh.........hhhhhhhhhhhh......hhhhh....hhhhhh...hhhhhhhhhhhhhhhh.hhhhhh.........eeeeeeee..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.............hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zxu B   7 ASLPKAIFLMGPTASGKTALAIELRKILPVELISVDSALIYKGMDIGTAKPNAEELLAAPHRLLDIRDPSQAYSAADFRRDALAEMADITAAGRIPLLVGGTMLYFKALLEGLSPLPSADPEVRARIEQQAAEQGWESLHRQLQEVDPVAAARIHPNDPQRLSRALEVFFISGKTLTELTQTSGDALPYQVHQFAIAPASRELLHQRIEQRFHQMLASGFEAEVRALFARGDLHTDLPSIRCVGYRQMWSYLEGEISYDEMVYRGVCATRQLAKRQITWLRGWEGVHWLDSEKPEQARDEVLQVV 311
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306

Chain C from PDB  Type:RNA  Length:74
                                                                                                          
                 2zxu C   1 GCCCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUUCCGAGUCCGGGCAC  74
                                    10        20        30        40        50        60        70

Chain D from PDB  Type:RNA  Length:69
                                                                                                     
                 2zxu D   1 GCCCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUUCCGAGUCCG  69
                                    10        20        30        40        50        60

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 2ZXU)

(no "CATH Domain" information available for 2ZXU)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: IPPT (3)

Escherichia coli (strain K12) (2)

1a	IPPT-2zxuB01	B:44-298
1b	IPPT-2zxuB02	B:44-298

Asymmetric Unit(hide GO term definitions)

Chain A,B (MIAA_ECOLI | P16384)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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: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:0034605	cellular response to heat	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
	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
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	2zxu
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	MIAA_ECOLI \| P16384	:	2zm5 3foz

2zm5	THE SAME PROTEIN/TRNA COMPLEX WITHOUT LIGAND

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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Pfam Domains (1, 2)

Gene Ontology (7, 7)

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