3TV1 - JenaLib

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Title :   CRYSTAL STRUCTURE OF RTCA.AMP PRODUCT COMPLEX

Authors :   A. K. Chakravarty, P. Smith, S. Shuman

Date :   19 Sep 11 (Deposition) - 28 Dec 11 (Release) - 18 Jan 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Cyclizing 3'-Phosphate Ends, Transferase, Cyclase Family (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. K. Chakravarty, P. Smith, S. Shuman
Structures Of Rna 3'-Phosphate Cyclase Bound To Atp Reveal The Mechanism Of Nucleotidyl Transfer And Metal-Assisted Catalysis.
Proc. Natl. Acad. Sci. Usa V. 108 21034 2011
PubMed-ID: 22167800 | Reference-DOI: 10.1073/PNAS.1115560108

Molecule 1 - RNA 3'-TERMINAL PHOSPHATE CYCLASE
	Chains	:	A, B
	EC Number	:	6.5.1.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	B4475, JW5688, RTCA, YHGJ, YHGK
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	RNA CYCLASE, RNA-3'-PHOSPHATE CYCLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 10)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	CL	1	Ligand/Ion	CHLORIDE ION
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	GOL	1	Ligand/Ion	GLYCEROL
5	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
6	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 5)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	GOL	1	Ligand/Ion	GLYCEROL
5	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
6	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
4	GOL	-1	Ligand/Ion	GLYCEROL
5	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
6	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:21 , GLN A:104 , SER A:129 , ALA A:130 , PRO A:131 , PHE A:251 , TYR A:284 , ASP A:287 , GLN A:288 , ASN A:309 , HOH A:428 , HOH A:509 , HOH A:538 , HOH A:565 , HOH A:566	BINDING SITE FOR RESIDUE AMP A 401
02	AC2	SOFTWARE	ARG B:21 , GLN B:104 , SER B:129 , ALA B:130 , PRO B:131 , PHE B:135 , PHE B:251 , TYR B:284 , ASP B:287 , GLN B:288 , ASN B:309 , HOH B:359 , HOH B:389 , HOH B:477 , HOH B:624	BINDING SITE FOR RESIDUE AMP B 401
03	AC3	SOFTWARE	HIS B:158 , LEU B:197 , HIS B:225 , HOH B:461 , HOH B:537 , HOH B:866 , HOH B:890	BINDING SITE FOR RESIDUE SO4 B 801
04	AC4	SOFTWARE	HIS A:158 , LEU A:197 , HIS A:225 , HOH A:502 , HOH A:526 , HOH A:541 , HOH A:827 , HOH A:828	BINDING SITE FOR RESIDUE SO4 A 802
05	AC5	SOFTWARE	GLU A:14 , ARG A:43 , HOH A:657 , HOH A:805 , HOH A:862 , HOH A:878	BINDING SITE FOR RESIDUE SO4 A 803
06	AC6	SOFTWARE	GLU B:14 , ARG B:43 , HOH B:575 , HOH B:614 , HOH B:823 , HOH B:865	BINDING SITE FOR RESIDUE SO4 B 804
07	AC7	SOFTWARE	THR B:125 , ASP B:126 , ALA B:133 , HOH B:728 , PEG B:991	BINDING SITE FOR RESIDUE CL B 851
08	AC8	SOFTWARE	ARG A:137 , ARG A:138 , ARG A:193	BINDING SITE FOR RESIDUE EDO A 901
09	AC9	SOFTWARE	GLU A:207 , ILE A:210 , ALA A:211 , HOH A:678 , HOH A:872	BINDING SITE FOR RESIDUE GOL A 951
10	BC1	SOFTWARE	ASP B:126 , PRO B:132 , ALA B:133 , ASP B:134 , LEU B:155 , HOH B:666 , CL B:851 , HOH B:890	BINDING SITE FOR RESIDUE PEG B 991

(no "SS Bond" information available for 3TV1)

Asymmetric Unit

No.	Residues
1	Tyr A:161	-	Pro A:162
2	Gly A:232	-	Pro A:233
3	Tyr B:161	-	Pro B:162
4	Gly B:232	-	Pro B:233

(no "SAP(SNP)/Variant" information available for 3TV1)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RTC	PS01287	RNA 3'-terminal phosphate cyclase signature.	RTCA_ECOLI	157-167	2	A:158-168 B:158-168

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RTC	PS01287	RNA 3'-terminal phosphate cyclase signature.	RTCA_ECOLI	157-167	1	A:158-168 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RTC	PS01287	RNA 3'-terminal phosphate cyclase signature.	RTCA_ECOLI	157-167	1	- B:158-168

(no "Exon" information available for 3TV1)

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:336
 aligned with RTCA_ECOLI | P46849 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:336
                                    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      
           RTCA_ECOLI     3 RMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSCHLLTNIAVVERFLPVRFSLIETDGVTRVSIE 338
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee.......hhhhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhhh.eee.......eeeee......eeeeeeeeeeeehhhhhhhhhhhhh.....eeeeeeee.......hhhhhhhhhhhhhhhhh.eeeeeeee........eeeeeeee...............eeeeeeeeeee..hhhhhhhhhhhhhhhh...eeeeeeehhhhh.eeeeeeeeee...eeeeeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh...eeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------RTC        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tv1 A   4 RMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSSNLLTNIAVVERFLPVRFSLIETDGVTRVSIE 339
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333

Chain B from PDB  Type:PROTEIN  Length:336
 aligned with RTCA_ECOLI | P46849 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:336
                                    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      
           RTCA_ECOLI     3 RMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSCHLLTNIAVVERFLPVRFSLIETDGVTRVSIE 338
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee.......hhhhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhhh.eee........eeee.......eeeeeeeeeeehhhhhhhhhhhhh.....eeeeeeee.......hhhhhhhhhhhhhhhhh.eeeeeeee........eeeeeeee.......ee......eeeeeeeeeee...hhhhhhhhhhhhhhh...eeeeeeehhhhh.eeeeeeeeee...eeeeeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhh...eeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------RTC        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tv1 B   4 RMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSSNLLTNIAVVERFLPVRFSLIETDGVTRVSIE 339
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333

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 3TV1)

(no "CATH Domain" information available for 3TV1)

(no "Pfam Domain" information available for 3TV1)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RTCA_ECOLI | P46849)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003963	RNA-3'-phosphate cyclase activity	Catalysis of the reaction: ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate.
	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:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	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.
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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	Cis Peptide Bonds
		Gly A:232 - Pro A:233	[ RasMol ]
		Gly B:232 - Pro B:233	[ RasMol ]
		Tyr A:161 - Pro A:162	[ RasMol ]
		Tyr B:161 - Pro B:162	[ RasMol ]

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	3tv1
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	RTCA_ECOLI \| P46849
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	6.5.1.4
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	RTCA_ECOLI \| P46849	:	1qmh 1qmi 3kgd 3tut 3tux 3tw3

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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