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Title :   CRYSTAL STRUCTURE OF THE A.FULGIDUS CCA-ADDING ENZYME IN COMPLEX WITH A G70A ARGINYL-TRNA MINIHELIX ENDING IN CCACC AND AMPCPP

Authors :   C. -D. Kuhn, L. Joshua-Tor

Date :   03 Dec 14 (Deposition) - 11 Feb 15 (Release) - 25 Feb 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

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

Keywords :   Protein-Rna Complex, Trna, Non-Coding Rna, Cca-Adding Enzyme, Nucleotidyltransferase, Ncrna, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. D. Kuhn, J. E. Wilusz, Y. Zheng, P. A. Beal, L. Joshua-Tor
On-Enzyme Refolding Permits Small Rna And Trna Surveillance By The Cca-Adding Enzyme.
Cell V. 160 644 2015
PubMed-ID: 25640237 | Reference-DOI: 10.1016/J.CELL.2015.01.005

Molecule 1 - CCA-ADDING ENZYME
	Chains	:	A, C
	EC Number	:	2.7.7.72
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22
	Expression System Strain	:	BL21(DE3)RIPL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	A. FULGIDUS CCA-ADDING ENZYME
	Gene	:	CCA, AF_2156
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	224325
	Strain	:	ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
	Synonym	:	CCA TRNA NUCLEOTIDYLTRANSFERASE,TRNA CCA-PYROPHOSPHORYLASE, TRNA ADENYLYL-/CYTIDYLYL- TRANSFERASE,TRNA NUCLEOTIDYLTRANSFERASE, TRNA-NT

Molecule 2 - G70A TRNA MINIHELIX ENDING IN CCACC
	Chains	:	B, D
	Engineered	:	YES
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

*Molecule 3 - RNA (5'-D(CPG)-3')*
	Chains	:	H
	Engineered	:	YES
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	H
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D	H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 10)

No.	Name	Count	Type	Full Name
1	APC	2	Ligand/Ion	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2	GOL	3	Ligand/Ion	GLYCEROL
3	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	MG	2	Ligand/Ion	MAGNESIUM ION
5	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
6	TAR	1	Ligand/Ion	D(-)-TARTARIC ACID

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	APC	1	Ligand/Ion	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2	GOL	2	Ligand/Ion	GLYCEROL
3	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
6	TAR	-1	Ligand/Ion	D(-)-TARTARIC ACID

Biological Unit 2 (4, 4)

No.	Name	Count	Type	Full Name
1	APC	1	Ligand/Ion	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2	GOL	1	Ligand/Ion	GLYCEROL
3	MES	-1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
6	TAR	1	Ligand/Ion	D(-)-TARTARIC ACID

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	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 , MG A:502 , A B:35 , C B:36 , C B:37	binding site for residue APC A 501
02	AC2	SOFTWARE	SER A:47 , GLU A:59 , ASP A:61 , APC A:501	binding site for residue MG A 502
03	AC3	SOFTWARE	ILE A:92 , TYR A:94	binding site for residue MES A 503
04	AC4	SOFTWARE	VAL A:200 , ARG A:209 , GLU A:222	binding site for residue GOL A 504
05	AC5	SOFTWARE	ARG A:317 , SER A:318 , GLU C:370	binding site for residue GOL A 505
06	AC6	SOFTWARE	GLY C:46 , SER C:47 , ARG C:50 , GLU C:59 , ASP C:61 , THR C:130 , HIS C:133 , LYS C:152 , TYR C:161 , TYR C:173 , ARG C:224 , MG C:502 , A D:35 , C D:36 , C D:37	binding site for residue APC C 501
07	AC7	SOFTWARE	SER C:47 , GLU C:59 , ASP C:61 , APC C:501	binding site for residue MG C 502
08	AC8	SOFTWARE	GLU C:311 , ARG C:344	binding site for residue GOL C 503
09	AC9	SOFTWARE	HIS A:240 , ARG A:243 , GLU A:244 , GLU A:247 , GLU C:352 , VAL C:355 , LYS C:356	binding site for residue TAR C 504
10	AD1	SOFTWARE	PHE A:349 , GLU A:352 , VAL A:355 , HIS C:240 , ARG C:243	binding site for residue PEG C 505

(no "SS Bond" information available for 4X4R)

(no "Cis Peptide Bond" information available for 4X4R)

(no "SAP(SNP)/Variant" information available for 4X4R)

(no "PROSITE Motif" information available for 4X4R)

(no "Exon" information available for 4X4R)

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:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eeeehhhhh........eeeeeeee....hhhhhhhhhhhhhhhhh.eee........eeeee..eeeeeeeee.............hhhhhhhhhh.....hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhh.....eeee.hhheeee....eeee..eeeee.....hhhhhhhhhhhhhhhhhh.hhhhh...ee...hhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee...eeeeeeee.......eeeeeeee..hhhhhhhhhhh......eee..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeehhhhhh..hhhhhhhhhh....ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x4r A   1 MKVEEILEKALELVIPDEEEVRKGREAEEELRRRLDELGVEYVFVGSYARNTWLKGSLEIDVFLLFPEEFSKEELRERGLEIGKAVLDSYEIRYAEHPYVHGVVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIKGKENEVRLLKGFLKANGIYGAEYKVRGFSGYLCELLIVFYGSFLETVKNARRWTRRTVIDVAKGEVRKGEEFFVVDPVDEKRNVAANLSLDNLARFVHLCREFMEAPSLGFFKPKHPLEIEPERLRKIVEERGTAVFAVKFRKPDIVDDNLYPQLERASRKIFEFLERENFMPLRSAFKASEEFCYLLFECQIKEISRVFRRMGPQFEDERNVKKFLSRNRAFRPFIENGRWWAFEMRKFTTPEEGVRSYASTHWHTLGKNVGESIREYFEIISGEKLFKEPVTAELCEMMGVKDSNSSSV 443
                                    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       440

Chain B from PDB  Type:RNA  Length:35
                                                                   
                 4x4r B   1 GGCCGCGGCAGGUUCGAGUCCUGCCGCGCGCCACC  37
                                    10        20       |32     
                                                      28|      
                                                       31

Chain C from PDB  Type:PROTEIN  Length:437
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeehhhhh........eeeeeeee....hhhhhhhhhhhhhhhhh.eee........eeeee..eeeeeeeee............hhhhhhhhhhh.....hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhh.....eeee.hhheeee....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
                 4x4r C   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 D from PDB  Type:RNA  Length:30
                                                              
                 4x4r D   1 GGCCGCGGCAGGUUCGAUCCUGCCGCCACC  37
                                    10      ||21   ||   37
                                           17|    25|     
                                            19     32

Chain H from PDB  Type:RNA  Length:2
                                  
                 4x4r H   1 CG   2

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 4X4R)

(no "CATH Domain" information available for 4X4R)

(no "Pfam Domain" information available for 4X4R)

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Description

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Ligands, Modified Residues, Ions (6, 10)

Sites (10, 10)

SS Bonds (0, 0)

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