3H37 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   THE STRUCTURE OF CCA-ADDING ENZYME APO FORM I

Authors :   Y. Toh, K. Tomita

Date :   16 Apr 09 (Deposition) - 13 Oct 09 (Release) - 05 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Transferase/Rna, Nucleotide-Binding, Nucleotidyltransferase, Rna- Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Toh, D. Takeshita, T. Numata, S. Fukai, O. Nureki, K. Tomita
Mechanism For The Definition Of Elongation And Termination By The Class Ii Cca-Adding Enzyme
Embo J. V. 28 3353 2009
PubMed-ID: 19745807 | Reference-DOI: 10.1038/EMBOJ.2009.260

Molecule 1 - TRNA NUCLEOTIDYL TRANSFERASE-RELATED PROTEIN
	Chains	:	A, B
	EC Number	:	2.7.7.25
	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
	Fragment	:	UNP RESIDUES 437-863
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	TRNA NUCLEOTIDYLTRANSFERASE, TRNA ADENYL-/CYTIDYL- TRANSFERASE, TRNA CCA-PYROPHOSPHORYLASE, TRNA-NT

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 19)

No.	Name	Count	Type	Full Name
1	MSE	19	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 19)

No.	Name	Count	Type	Full Name
1	MSE	19	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 10)

No.	Name	Count	Type	Full Name
1	MSE	10	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 9)

No.	Name	Count	Type	Full Name
1	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3H37)

(no "SS Bond" information available for 3H37)

Asymmetric Unit

No.	Residues
1	Pro B:115	-	Asp B:116
2	Lys B:386	-	Gly B:387

(no "SAP(SNP)/Variant" information available for 3H37)

(no "PROSITE Motif" information available for 3H37)

(no "Exon" information available for 3H37)

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:415
 aligned with Q9WZH4_THEMA | Q9WZH4 from UniProtKB/TrEMBL  Length:863

    Alignment length:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     863 
                                   445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       | 
         Q9WZH4_THEMA   436 GQIFRDVSKLLVERVDPKILNLFRLLGKFGDEVNMPVYVVGGFVRDLLLGIKNLDIDIVVEGNALEFAEYAKRFLPGKLVKHDKFMTASLFLKGGLRIDIATARLEYYESPAKLPDVEMSTIKKDLYRRDFTINAMAIKLNPKDFGLLIDFFGGYRDLKEGVIRVLHTLSFVDDPTRILRAIRFEQRFDFRIEETTERLLKQAVEEGYLERTTGPRLRQELEKILEEKNPLKSIRRMAQFDVIKHLFPKTYYTPSMDEKMENLFRNIPWVEENFGEVDRFYAVLHVFLEFYDDESWKEVRDRYSLRRNLINEIRHVEKSAPALLEMLSERVPASFVYPLVKGVSNETICHFLAYLSGEKEGLFKSYLLKIKNTKLEKINGEYLIRKGITSGKIIGEVLEKILMKKLDGDTRDEEEILEEVLASLETEG-   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeehhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhh.....eeeee..hhhhhhhhhhh...eeee.......eeeee....eeeeee.--------------...hhhhhhh...hhhhh.eee.......eee...hhhhhhhh.ee.....hhhhhh.hhhhhhhhhhhhhh.eehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhh........hhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h37 A   1 mQIFRDVSKLLVERVDPKILNLFRLLGKFGDEVNmPVYVVGGFVRDLLLGIKNLDIDIVVEGNALEFAEYAKRFLPGKLVKHDKFmTASLFLKGGLRIDIATA--------------EmSTIKKDLYRRDFTINAmAIKLNPKDFGLLIDFFGGYRDLKEGVIRVLHTLSFVDDPTRILRAIRFEQRFDFRIEETTERLLKQAVEEGYLERTTGPRLRQELEKILEEKNPLKSIRRmAQFDVIKHLFPKTYYTPSmDEKmENLFRNIPWVEENFGEVDRFYAVLHVFLEFYDDESWKEVRDRYSLRRNLINEIRHVEKSAPALLEmLSERVPASFVYPLVKGVSNETICHFLAYLSGEKEGLFKSYLLKIKNTKLEKINGEYLIRKGITSGKIIGEVLEKILmKKLDGDTRDEEEILEEVLASLETEGK 429
                            |       10        20        30    |   40        50        60        70        80     |  90       100  |      -       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         
                            |                                35-MSE                                             86-MSE          103            118|              136-MSE                                                                                              237-MSE            256-MSE                                                               326-MSE                                                                      403-MSE                      
                            1-MSE                                                                                                               119-MSE                                                                                                                                      260-MSE

Chain B from PDB  Type:PROTEIN  Length:421
 aligned with Q9WZH4_THEMA | Q9WZH4 from UniProtKB/TrEMBL  Length:863

    Alignment length:430
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    863   
                                   446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856      |  -
         Q9WZH4_THEMA   437 QIFRDVSKLLVERVDPKILNLFRLLGKFGDEVNMPVYVVGGFVRDLLLGIKNLDIDIVVEGNALEFAEYAKRFLPGKLVKHDKFMTASLFLKGGLRIDIATARLEYYESPAKLPDVEMSTIKKDLYRRDFTINAMAIKLNPKDFGLLIDFFGGYRDLKEGVIRVLHTLSFVDDPTRILRAIRFEQRFDFRIEETTERLLKQAVEEGYLERTTGPRLRQELEKILEEKNPLKSIRRMAQFDVIKHLFPKTYYTPSMDEKMENLFRNIPWVEENFGEVDRFYAVLHVFLEFYDDESWKEVRDRYSLRRNLINEIRHVEKSAPALLEMLSERVPASFVYPLVKGVSNETICHFLAYLSGEKEGLFKSYLLKIKNTKLEKINGEYLIRKGITSGKIIGEVLEKILMKKLDGDTRDEEEILEEVLASLETEG---   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhh.....eeeee..hhhhhhhhhhhh..eeeeee....eeeeee....eeeeee...---------..hhhhhhhhhhhh..hhhhh.eee.hhhhh.eee...hhhhhhhh.ee.....hhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhh.......hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h37 B   2 QIFRDVSKLLVERVDPKILNLFRLLGKFGDEVNmPVYVVGGFVRDLLLGIKNLDIDIVVEGNALEFAEYAKRFLPGKLVKHDKFmTASLFLKGGLRIDIATARL---------PDVEmSTIKKDLYRRDFTINAmAIKLNPKDFGLLIDFFGGYRDLKEGVIRVLHTLSFVDDPTRILRAIRFEQRFDFRIEETTERLLKQAVEEGYLERTTGPRLRQELEKILEEKNPLKSIRRmAQFDVIKHLFPKTYYTPSmDEKmENLFRNIPWVEENFGEVDRFYAVLHVFLEFYDDESWKEVRDRYSLRRNLINEIRHVEKSAPALLEmLSERVPASFVYPLVKGVSNETICHFLAYLSGEKEGLFKSYLLKIKNTKLEKINGEYLIRKGITSGKIIGEVLEKILmKKLDGDTRDEEEILEEVLASLETEGKLA 431
                                    11        21        31   |    41        51        61        71        81    |   91       101   |     -   |   121       131    |  141       151       161       171       181       191       201       211       221       231     | 241       251    |  261       271       281       291       301       311       321    |  331       341       351       361       371       381       391       401 |     411       421       431
                                                            35-MSE                                             86-MSE            105       115   |              136-MSE                                                                                              237-MSE            256-MSE                                                               326-MSE                                                                      403-MSE                        
                                                                                                                                               119-MSE                                                                                                                                      260-MSE

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 3H37)

(no "CATH Domain" information available for 3H37)

(no "Pfam Domain" information available for 3H37)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9WZH4_THEMA | Q9WZH4)

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:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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: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: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.

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	Sites
(no "Sites" information available for 3h37)

	Cis Peptide Bonds
		Lys B:386 - Gly B:387	[ RasMol ]
		Pro B:115 - Asp B:116	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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Access by PDB/NDB ID
	3h37
		Family and Domain Information	:	ProDom \| SYSTERS
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		Orientation in Membranes	:	OPM
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	Q9WZH4_THEMA \| Q9WZH4
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	2.7.7.25
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UniProtKB/TrEMBL
	Q9WZH4_THEMA \| Q9WZH4	:	3h38 3h39 3h3a 5hc9

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 19)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (12, 12)

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