2ZH9 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

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Title :   COMPLEX STRUCTURE OF AFCCA WITH TRNAMINIDU

Authors :   Y. Toh, K. Tomita

Date :   01 Feb 08 (Deposition) - 05 Aug 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym./Biol. Unit : A,B

Keywords :   Transferase/Rna, Atp-Binding, Magnesium, Metal-Binding, Nucleotide-Binding, Nucleotidyltransferase, Rna Repair, Rna- Binding, Trna Processing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Toh, T. Numata, K. Watanabe, D. Takeshita, O. Nureki, K. Tomita
Molecular Basis For Maintenance Of Fidelity During The Cca-Adding Reaction By A Cca-Adding Enzyme
Embo J. V. 27 1944 2008
PubMed-ID: 18583961 | Reference-DOI: 10.1038/EMBOJ.2008.124
(for further references see the PDB file header)

Molecule 1 - CCA-ADDING ENZYME
	Chains	:	A
	EC Number	:	2.7.7.25, 2.7.7.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-22B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	2234
	Synonym	:	TRNA NUCLEOTIDYLTRANSFERASE, TRNA ADENYLYL- /CYTIDYLYL- TRANSFERASE, TRNA CCA-PYROPHOSPHORYLASE, TRNA- NT

Molecule 2 - TRNA (33-MER)
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:47 , THR A:52 , TRP A:53 , LEU A:54 , SER A:57 , LYS A:152 , TYR A:161	BINDING SITE FOR RESIDUE SO4 A 438
2	AC2	SOFTWARE	ARG A:299 , ARG A:302 , LYS A:303	BINDING SITE FOR RESIDUE SO4 A 439

(no "SS Bond" information available for 2ZH9)

(no "Cis Peptide Bond" information available for 2ZH9)

(no "SAP(SNP)/Variant" information available for 2ZH9)

(no "PROSITE Motif" information available for 2ZH9)

(no "Exon" information available for 2ZH9)

Asymmetric/Biological 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:437
 aligned with CCA_ARCFU | O28126 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:437
                                    10        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       390       400       410       420       430       
            CCA_ARCFU     1 MKVEEILEKALELVIPDEEEVRKGREAEEELRRRLDELGVEYVFVGSYARNTWLKGSLEIDVFLLFPEEFSKEELRERGLEIGKAVLDSYEIRYAEHPYVHGVVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIKGKENEVRLLKGFLKANGIYGAEYKVRGFSGYLCELLIVFYGSFLETVKNARRWTRRTVIDVAKGEVRKGEEFFVVDPVDEKRNVAANLSLDNLARFVHLCREFMEAPSLGFFKPKHPLEIEPERLRKIVEERGTAVFAVKFRKPDIVDDNLYPQLERASRKIFEFLERENFMPLRSAFKASEEFCYLLFECQIKEISRVFRRMGPQFEDERNVKKFLSRNRAFRPFIENGRWWAFEMRKFTTPEEGVRSYASTHWHTLGKNVGESIREYFEIISGEKLFKEPVTAELCEMMGVKD 437
               SCOP domains d2zh9a2 A:1-142 tRNA nucleotidyltransferase, N-terminal domain                                                                                d2zh9a1 A:143-257 tRNA nucleotidyltransferase, second domain                                                       d2zh9a3 A:258-437 tRNA nucleotidyltransferase, C-terminal domain                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------NTP_transf_2-2zh9A01 A:25-133                                                                                ------------tRNA_NucTransf2-2zh9A02 A:146-256                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....eeee.............eeeeeeee....hhhhhhhhhhhhhhhhh.eeeee.....eeeeee..eeeeeeeee.............hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh.....eeee.hhheeee....eee.............hhhhhhhhhhhhhhhhhh..hhhhh.......hhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee...eeeeeeee.......eeeeeeee..hhhhhhhhh........eee..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeehhhhhhh.hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zh9 A   1 MKVEEILEKALELVIPDEEEVRKGREAEEELRRRLDELGVEYVFVGSYARNTWLKGSLEIDVFLLFPEEFSKEELRERGLEIGKAVLDSYEIRYAEHPYVHGVVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIKGKENEVRLLKGFLKANGIYGAEYKVRGFSGYLCELLIVFYGSFLETVKNARRWTRRTVIDVAKGEVRKGEEFFVVDPVDEKRNVAANLSLDNLARFVHLCREFMEAPSLGFFKPKHPLEIEPERLRKIVEERGTAVFAVKFRKPDIVDDNLYPQLERASRKIFEFLERENFMPLRSAFKASEEFCYLLFECQIKEISRVFRRMGPQFEDERNVKKFLSRNRAFRPFIENGRWWAFEMRKFTTPEEGVRSYASTHWHTLGKNVGESIREYFEIISGEKLFKEPVTAELCEMMGVKD 437
                                    10        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       390       400       410       420       430

Chain B from PDB  Type:RNA  Length:33
                                                                 
                 2zh9 B   1 GGCCCGGGGCGGUUCGAUUCCGCCCUGGGCCAU  33
                                    10        20        30

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 "CATH Domain" information available for 2ZH9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CCA_ARCFU | O28126)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0052929	ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity	Catalysis of the reaction: a tRNA with a 3' CC end + ATP = a tRNA with a 3' CCA end + diphosphate.
	GO:0052928	CTP:3'-cytidine-tRNA cytidylyltransferase activity	Catalysis of the reaction: a tRNA with a 3' cytidine + CTP = a tRNA with a 3' CC end + diphosphate.
	GO:0052927	CTP:tRNA cytidylyltransferase activity	Catalysis of the reaction: a tRNA precursor + CTP = a tRNA with a 3' cytidine end + diphosphate.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0004810	tRNA adenylyltransferase activity	Catalysis of the reaction: ATP + tRNA(n) = diphosphate + tRNA(n+1).
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
	GO:0016437	tRNA cytidylyltransferase activity	Catalysis of the reaction: CTP + tRNA(n) = diphosphate + tRNA(n+1).
	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:0031123	RNA 3'-end processing	Any process involved in forming the mature 3' end of an RNA molecule.
	GO:0042245	RNA repair	Any process that results in the repair of damaged RNA.
	GO:0001680	tRNA 3'-terminal CCA addition	Post-transcriptional addition of the terminal 3' CCA sequence to a tRNA which does not encode this sequence within the primary transcript. CCA addition proceeds by the sequential addition of CTP, CTP, and then ATP to the 3' end of the tRNA, yielding a diphosphate with each nucleotide addition.
	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/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (3, 3)

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Pfam Domains (2, 2)

Gene Ontology (17, 17)

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