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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF BACILLUS STEAROTHERMOPHILUS CCA-ADDING ENZYME IN COMPLEX WITH CTP

Authors :   F. Li, Y. Xiong, J. Wang, H. D. Cho, A. M. Weiner, T. A. Steitz

Date :   23 Aug 02 (Deposition) - 13 Dec 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.52

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

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

Reference :   F. Li, Y. Xiong, J. Wang, H. D. Cho, K. Tomita, A. M. Weiner, T. A. Steitz
Crystal Structures Of The Bacillus Stearothermophilus Cca-Adding Enzyme And Its Complexes With Atp Or Ctp
Cell(Cambridge, Mass. ) V. 111 815 2002
PubMed-ID: 12526808 | Reference-DOI: 10.1016/S0092-8674(02)01115-7

Molecule 1 - TRNA CCA-ADDING ENZYME
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	GEOBACILLUS STEAROTHERMOPHILUS
	Organism Taxid	:	1422

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	CTP	2	Ligand/Ion	CYTIDINE-5'-TRIPHOSPHATE
2	MG	4	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CTP A:5501	BINDING SITE FOR RESIDUE MG A 5601
2	AC2	SOFTWARE	ASP A:40 , ALA A:77 , HOH A:5612 , LYS B:58	BINDING SITE FOR RESIDUE MG A 5611
3	AC3	SOFTWARE	CTP B:6501	BINDING SITE FOR RESIDUE MG B 6601
4	AC4	SOFTWARE	ALA B:77 , HOH B:6612	BINDING SITE FOR RESIDUE MG B 6611
5	AC5	SOFTWARE	GLY A:26 , GLY A:27 , ARG A:30 , ARG A:110 , ARG A:111 , ASP A:112 , ASN A:116 , ASP A:154 , ARG A:157 , ARG A:160 , ARG A:163 , PHE A:164 , GLU A:167 , MG A:5601	BINDING SITE FOR RESIDUE CTP A 5501
6	AC6	SOFTWARE	GLY B:27 , ARG B:30 , ARG B:111 , ASP B:112 , ASN B:116 , ASP B:154 , ARG B:157 , ARG B:160 , ARG B:163 , PHE B:164 , GLU B:167 , MG B:6601	BINDING SITE FOR RESIDUE CTP B 6501

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

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

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

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

(no "Exon" information available for 1MIY)

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:395
 aligned with CCA_GEOSE | Q7SIB1 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:404
                                    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    
            CCA_GEOSE     1 MKPPFQEALGIIQQLKQHGYDAYFVGGAVRDLLLGRPIGDVDIATSALPEDVMAIFPKTIDVGSKHGTVVVVHKGKAYEVTTFKTDGDYEDYRRPESVTFVRSLEEDLKRRDFTMNAIAMDEYGTIIDPFGGREAIRRRIIRTVGEAEKRFREDALRMMRAVRFVSELGFALAPDTEQAIVQNAPLLAHISVERMTMEMEKLLGGPFAARALPLLAETGLNAYLPGLAGKEKQLRLAAAYRWPWLAAREERWALLCHALGVQESRPFLRAWKLPNKVVDEAGAILTALADIPRPEAWTNEQLFSAGLERALSVETVRAAFTGAPPGPWHEKLRRRFASLPIKTKGELAVNGKDVIEWVGKPAGPWVKEALDAIWRAVVNGEVENEKERIYAWLMERNRTREKNC 404
               SCOP domains d1miya2 A:1-139 tRNA CCA-adding enzyme, head domain                                                                                        d1miya1 A:140-404 tRNA CCA-adding enzyme, C-terminal domains                                                                                                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...eeeehhhhhhhhhh......eeee..hhhhhhhhh..eeeee....eeeeee..eeeeeee.ee..---------..ee..hhhhhhh...hhhhh.ee.....ee...hhhhhhhhhee....hhhhhhhhh.hhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh............hhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1miy A   1 MKPPFQEALGIIQQLKQHGYDAYFVGGAVRDLLLGRPIGDVDIATSALPEDVMAIFPKTIDVGSKHGTVVVVHKGKAYEVTTFKTDG---------SVTFVRSLEEDLKRRDFTMNAIAMDEYGTIIDPFGGREAIRRRIIRTVGEAEKRFREDALRMMRAVRFVSELGFALAPDTEQAIVQNAPLLAHISVERMTMEMEKLLGGPFAARALPLLAETGLNAYLPGLAGKEKQLRLAAAYRWPWLAAREERWALLCHALGVQESRPFLRAWKLPNKVVDEAGAILTALADIPRPEAWTNEQLFSAGLERALSVETVRAAFTGAPPGPWHEKLRRRFASLPIKTKGELAVNGKDVIEWVGKPAGPWVKEALDAIWRAVVNGEVENEKERIYAWLMERNRTREKNC 404
                                    10        20        30        40        50        60        70        80      |  -      |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    
                                                                                                                 87        97

Chain B from PDB  Type:PROTEIN  Length:395
 aligned with CCA_GEOSE | Q7SIB1 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:404
                                    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    
            CCA_GEOSE     1 MKPPFQEALGIIQQLKQHGYDAYFVGGAVRDLLLGRPIGDVDIATSALPEDVMAIFPKTIDVGSKHGTVVVVHKGKAYEVTTFKTDGDYEDYRRPESVTFVRSLEEDLKRRDFTMNAIAMDEYGTIIDPFGGREAIRRRIIRTVGEAEKRFREDALRMMRAVRFVSELGFALAPDTEQAIVQNAPLLAHISVERMTMEMEKLLGGPFAARALPLLAETGLNAYLPGLAGKEKQLRLAAAYRWPWLAAREERWALLCHALGVQESRPFLRAWKLPNKVVDEAGAILTALADIPRPEAWTNEQLFSAGLERALSVETVRAAFTGAPPGPWHEKLRRRFASLPIKTKGELAVNGKDVIEWVGKPAGPWVKEALDAIWRAVVNGEVENEKERIYAWLMERNRTREKNC 404
               SCOP domains d1miyb2 B:1-139 tRNA CCA-adding enzyme, head domain                                                                                        d1miyb1 B:140-404 tRNA CCA-adding enzyme, C-terminal domains                                                                                                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------PolyA_pol-1miyB03 B:22-142                                                                                               --------------------------PolyA_pol_RNAbd-1miyB05 B:169-230                             --------------tRNA_NucTran2_2-1miyB01 B:245-393                                                                                                                    ----------- Pfam domains (1)
           Pfam domains (2) ---------------------PolyA_pol-1miyB04 B:22-142                                                                                               --------------------------PolyA_pol_RNAbd-1miyB06 B:169-230                             --------------tRNA_NucTran2_2-1miyB02 B:245-393                                                                                                                    ----------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhh...eeeehhhhhhhhhh......eeee..hhhhhhhhh..eeeee....eeeeee..eeeeeee.ee..---------..ee..hhhhhhh...hhhhh.eee.........hhhhhhhhhee....hhhhhhhhh.hhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.............hhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1miy B   1 MKPPFQEALGIIQQLKQHGYDAYFVGGAVRDLLLGRPIGDVDIATSALPEDVMAIFPKTIDVGSKHGTVVVVHKGKAYEVTTFKTDG---------SVTFVRSLEEDLKRRDFTMNAIAMDEYGTIIDPFGGREAIRRRIIRTVGEAEKRFREDALRMMRAVRFVSELGFALAPDTEQAIVQNAPLLAHISVERMTMEMEKLLGGPFAARALPLLAETGLNAYLPGLAGKEKQLRLAAAYRWPWLAAREERWALLCHALGVQESRPFLRAWKLPNKVVDEAGAILTALADIPRPEAWTNEQLFSAGLERALSVETVRAAFTGAPPGPWHEKLRRRFASLPIKTKGELAVNGKDVIEWVGKPAGPWVKEALDAIWRAVVNGEVENEKERIYAWLMERNRTREKNC 404
                                    10        20        30        40        50        60        70        80      |  -      |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    
                                                                                                                 87        97

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 1MIY)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CCA_GEOSE | Q7SIB1)

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:0006396	RNA processing	Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
	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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(no "Cis Peptide Bonds" information available for 1miy)

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (0, 0)

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