1SZ1 | PR0126 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

Title :   MECHANISM OF CCA-ADDING ENZYMES SPECIFICITY REVEALED BY CRYSTAL STRUCTURES OF TERNARY COMPLEXES

Authors :   Y. Xiong, T. A. Steitz

Date :   02 Apr 04 (Deposition) - 10 Aug 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   6.21

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

Keywords :   Cca-Adding Enzyme, Specificity, Trna, Complex, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Xiong, T. A. Steitz
Mechanism Of Transfer Rna Maturation By Cca-Adding Enzyme Without Using An Oligonucleotide Template.
Nature V. 430 640 2004
PubMed-ID: 15295590 | Reference-DOI: 10.1038/NATURE02711

Molecule 1 - T-RNA (76-MER)
	Chains	:	E, F
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - TRNA NUCLEOTIDYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.7.7.25
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	2234
	Synonym	:	TRNA ADENYLYLTRANSFERASE, TRNA CCA-PYROPHOSPHORYLASE, CCA- ADDING ENZYME

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (11, 28)

No.	Name	Count	Type	Full Name
1	1MA	2	Mod. Nucleotide	6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE
2	2MG	2	Mod. Nucleotide	2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
3	5MC	4	Mod. Nucleotide	5-METHYLCYTIDINE-5'-MONOPHOSPHATE
4	5MU	2	Mod. Nucleotide	5-METHYLURIDINE 5'-MONOPHOSPHATE
5	7MG	2	Mod. Nucleotide	7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE
6	H2U	4	Mod. Nucleotide	5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
7	M2G	2	Mod. Nucleotide	N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
8	OMC	2	Mod. Nucleotide	O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
9	OMG	2	Mod. Nucleotide	O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
10	PSU	4	Mod. Nucleotide	PSEUDOURIDINE-5'-MONOPHOSPHATE
11	YG	2	Mod. Residue	WYBUTOSINE

(no "Site" information available for 1SZ1)

(no "SS Bond" information available for 1SZ1)

(no "Cis Peptide Bond" information available for 1SZ1)

(no "SAP(SNP)/Variant" information available for 1SZ1)

(no "PROSITE Motif" information available for 1SZ1)

(no "Exon" information available for 1SZ1)

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 d1sz1a2 A:1-142 tRNA nucleotidyltransferase, N-terminal domain                                                                                d1sz1a1 A:143-257 tRNA nucleotidyltransferase, second domain                                                       d1sz1a3 A:258-437 tRNA nucleotidyltransferase, C-terminal domain                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeehhhhh........eeeeeee.....hhhhhhhhhhhhhhhhh.eeeee.....eeeeee..eeeeeee............hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh............hhhhhhhhhhhhh..hhhhhhhh.....eeee....eeee....eee.............hhhhhhhhhhhhhhhhhh.hhhhh........hhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee...eeeeeeee.......eeeeeeee..hhhhhhhhhhh......ee...eeeeeee....hhhhhhhhhhhhh....hhhhhhhhhhh.eeeehhhhhh..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sz1 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: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 d1sz1b2 B:1-142 tRNA nucleotidyltransferase, N-terminal domain                                                                                d1sz1b1 B:143-257 tRNA nucleotidyltransferase, second domain                                                       d1sz1b3 B:258-437 tRNA nucleotidyltransferase, C-terminal domain                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------NTP_transf_2-1sz1B01 B:25-133                                                                                ------------tRNA_NucTransf2-1sz1B03 B:146-256                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------NTP_transf_2-1sz1B02 B:25-133                                                                                ------------tRNA_NucTransf2-1sz1B04 B:146-256                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeehhhhh........eeeeeee.....hhhhhhhhhhhhhhhhh.eeeee.....eeeeee..eeeeeee............hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh............hhhhhhhhhhhhh..hhhhhhhh.....eeee....eeee....eee.............hhhhhhhhhhhhhhhhhh.hhhhh........hhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee...eeeeeeee.......eeeeeeee..hhhhhhhhhhh......ee...eeeeeee....hhhhhhhhhhhhh....hhhhhhhhhhh.eeeehhhhhh..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sz1 B   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 E from PDB  Type:RNA  Length:76
                                                                                                            
                 1sz1 E   1 GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAucUGGAGgUCcUGUGuuCGaUCCACAGAAUUCGCACCA  76
                                    10     || 20     |  30 | |  | 40     |  50   ||  |60        70      
                                    10-2MG ||       26-M2G | |  | ||     |  |    55-PSU                 
                                          16-H2U          32-OMC| ||     |  |    |  58-1MA              
                                           17-H2U           34-OMG||     |  |    |                      
                                                               37-YG     |  |    |                      
                                                                 39-PSU  |  |    |                      
                                                                  40-5MC |  |    |                      
                                                                        46-7MG   |                      
                                                                           49-5MC|                      
                                                                                54-5MU

Chain F from PDB  Type:RNA  Length:76
                                                                                                            
                 1sz1 F   1 GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAucUGGAGgUCcUGUGuuCGaUCCACAGAAUUCGCACCA  76
                                    10     || 20     |  30 | |  | 40     |  50   ||  |60        70      
                                    10-2MG ||       26-M2G | |  | ||     |  |    55-PSU                 
                                          16-H2U          32-OMC| ||     |  |    |  58-1MA              
                                           17-H2U           34-OMG||     |  |    |                      
                                                               37-YG     |  |    |                      
                                                                 39-PSU  |  |    |                      
                                                                  40-5MC |  |    |                      
                                                                        46-7MG   |                      
                                                                           49-5MC|                      
                                                                                54-5MU

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 1SZ1)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		1MA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		2MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		5MC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		5MU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		7MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		H2U	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		M2G	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		OMC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		OMG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PSU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		YG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 1sz1)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1sz1)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1sz1
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	CCA_ARCFU \| O28126
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.7.25
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	CCA_ARCFU \| O28126
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (11, 28)

Sites (0, 0)

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

Classification and Annotation

SCOP Domains (3, 6)

CATH Domains (0, 0)

Pfam Domains (2, 4)

Gene Ontology (17, 17)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File