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Title :   HOW THE CCA-ADDING ENZYME SELECTS ADENINE OVER CYTOSINE IN POSITION 76 OF TRNA

Authors :   B. C. Pan, Y. Xiong, T. A. Steitz

Date :   16 Sep 10 (Deposition) - 01 Dec 10 (Release) - 01 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.98

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

Keywords :   Protein-Rna, Rossmann Fold, Cca-Adding, Trna, Nucleotidyltransfer, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Pan, Y. Xiong, T. A. Steitz
How The Cca-Adding Enzyme Selects Adenine Over Cytosine At Position 76 Of Trna.
Science V. 330 937 2010
PubMed-ID: 21071662 | Reference-DOI: 10.1126/SCIENCE.1194985

Molecule 1 - CCA-ADDING ENZYME
	Chains	:	A
	EC Number	:	2.7.7.25, 2.7.7.21
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	2234
	Synonym	:	TRNA NUCLEOTIDYLTRANSFERASE, TRNA ADENYLYL-/CYTIDYLYL- TRANSFERASE, TRNA CCA-PYROPHOSPHORYLASE, TRNA-NT

Molecule 2 - RNA (34-MER)
	Chains	:	C
	Engineered	:	YES
	Other Details	:	CHEMISTRY SYNTHESIS
	Synonym	:	TRNA NUCLEOTIDYLTRANSFERASE, TRNA ADENYLYL-/CYTIDYLYL- TRANSFERASE, TRNA CCA-PYROPHOSPHORYLASE, TRNA-NT
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 6)

No.	Name	Count	Type	Full Name
1	APC	1	Ligand/Ion	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	APC	2	Ligand/Ion	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:1 , HOH A:2 , GLY A:46 , SER A:47 , ARG A:50 , GLU A:59 , ASP A:61 , THR A:130 , HIS A:133 , LYS A:152 , TYR A:161 , ARG A:224 , HOH A:448 , HOH A:519 , HOH A:543 , HOH A:561 , HOH A:567 , HOH A:572 , MG A:601 , A C:32 , C C:33 , C C:34	BINDING SITE FOR RESIDUE APC A 501
2	AC2	SOFTWARE	ARG A:299 , ARG A:302 , LYS A:303	BINDING SITE FOR RESIDUE SO4 A 503
3	AC3	SOFTWARE	SER A:47 , GLU A:59 , ASP A:61 , APC A:501	BINDING SITE FOR RESIDUE MG A 601
4	AC4	SOFTWARE	VAL A:40 , GLU A:41 , LEU A:64 , LEU A:65 , PHE A:66	BINDING SITE FOR RESIDUE EDO A 701
5	AC5	SOFTWARE	ARG A:140 , ILE A:408 , ARG A:409 , TYR A:411 , PHE A:412	BINDING SITE FOR RESIDUE EDO A 702
6	AC6	SOFTWARE	ILE A:123 , LYS A:124 , SER A:125 , ALA A:126 , HOH A:545	BINDING SITE FOR RESIDUE EDO A 703

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

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

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

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

(no "Exon" information available for 3OVA)

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:430
 aligned with CCA_ARCFU | O28126 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:435
                                    12        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       422       432     
            CCA_ARCFU     3 VEEILEKALELVIPDEEEVRKGREAEEELRRRLDELGVEYVFVGSYARNTWLKGSLEIDVFLLFPEEFSKEELRERGLEIGKAVLDSYEIRYAEHPYVHGVVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIKGKENEVRLLKGFLKANGIYGAEYKVRGFSGYLCELLIVFYGSFLETVKNARRWTRRTVIDVAKGEVRKGEEFFVVDPVDEKRNVAANLSLDNLARFVHLCREFMEAPSLGFFKPKHPLEIEPERLRKIVEERGTAVFAVKFRKPDIVDDNLYPQLERASRKIFEFLERENFMPLRSAFKASEEFCYLLFECQIKEISRVFRRMGPQFEDERNVKKFLSRNRAFRPFIENGRWWAFEMRKFTTPEEGVRSYASTHWHTLGKNVGESIREYFEIISGEKLFKEPVTAELCEMMGVKD 437
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeehhhhhh.......eeeeeeee....hhhhhhhhhhhhhhhhh.eee........eeeee..eeeeeeeee.............hhhhhhhhhhh....hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh.....eeee....eeee....eeee..eeeee.....hhhhhhhhhhhhhhhhhh.hhhhhh.-----.hhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee...eeeeeeee.......eeeeeeee..hhhhhhhhhhh......eee..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeehhhhhh..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ova A   3 VEEILEKALELVIPDEEEVRKGREAEEELRRRLDELGVEYVFVGSYARNTWLKGSLEIDVFLLFPEEFSKEELRERGLEIGKAVLDSYEIRYAEHPYVHGVVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIKGKENEVRLLKGFLKANGIYGAEYKVRGFSGYLCELLIVFYGSFLETVKNARRWTRRTVIDVAKGEVRKGEEFFVVDPVDEKRNVAANLSLDNLARFVHLCREFMEAPSLGFFKP-----IEPERLRKIVEERGTAVFAVKFRKPDIVDDNLYPQLERASRKIFEFLERENFMPLRSAFKASEEFCYLLFECQIKEISRVFRRMGPQFEDERNVKKFLSRNRAFRPFIENGRWWAFEMRKFTTPEEGVRSYASTHWHTLGKNVGESIREYFEIISGEKLFKEPVTAELCEMMGVKD 437
                                    12        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       422       432     
                                                                                                                                                                                                                                                                                       256   262

Chain C from PDB  Type:RNA  Length:34
                                                                  
                 3ova C   1 GGAAGUAGAUGGUUCAAGUCCAUUUACUUCCACC  34
                                    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 "SCOP Domain" information available for 3OVA)

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

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

Asymmetric 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 Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ova)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2.7.7.25
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (17, 17)

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