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Title :   CRYSTAL STRUCTURE OF RNA 3'-TERMINAL PHOSPHATE CYCLASE, AN UBIQUITOUS ENZYME WITH UNUSUAL TOPOLOGY

Authors :   G. J. Palm, E. Billy, W. Filipowicz, A. Wlodawer

Date :   28 Sep 99 (Deposition) - 11 Jan 00 (Release) - 17 Apr 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   2'3'Cyclic Phosphate Rna, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. J. Palm, E. Billy, W. Filipowicz, A. Wlodawer
Crystal Structure Of Rna 3'-Terminal Phosphate Cyclase, A Ubiquitous Enzyme With Unusual Topology
Structure V. 8 13 2000
PubMed-ID: 10673421 | Reference-DOI: 10.1016/S0969-2126(00)00076-9

Molecule 1 - RNA 3'-TERMINAL PHOSPHATE CYCLASE
	Cellular Location	:	CYTOPLASM
	Chains	:	A, B
	EC Number	:	6.5.1.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Gene	:	RTCA
	Expression System Plasmid	:	PET-11D_ECOLI CYCLASE
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET-11D
	Expression System Vector Type	:	PLASMID
	Gene	:	RTCA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K-12
	Synonym	:	RNA CYCLASE, RNA-3'-PHOSPHATE CYCLASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CIT	2	Ligand/Ion	CITRIC ACID
2	DTO	1	Ligand/Ion	1-HYDROXYSULFANYL-4-MERCAPTO-BUTANE-2,3-DIOL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:14 , GLY A:16 , GLY A:17 , ARG A:21 , ARG A:40 , ARG A:43 , GLN A:51 , HIS A:52	BINDING SITE FOR RESIDUE CIT A 401
2	AC2	SOFTWARE	GLY B:16 , GLY B:17 , ARG B:21 , ARG B:40 , ARG B:43 , HIS B:52 , HOH B:2215 , HOH B:2216	BINDING SITE FOR RESIDUE CIT B 401
3	AC3	SOFTWARE	GLY B:234 , ASN B:235 , GLY B:254 , GLU B:255 , LYS B:256 , VAL B:258 , VAL B:263 , HOH B:2176	BINDING SITE FOR RESIDUE DTO B 402

Asymmetric/Biological Unit

No.	Residues
1	A:308	-	B:308

Asymmetric/Biological 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 1QMH)

Asymmetric/Biological 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

(no "Exon" information available for 1QMH)

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:334
 aligned with RTCA_ECOLI | P46849 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:334
                                    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    
           RTCA_ECOLI     4 MIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSCHLLTNIAVVERFLPVRFSLIETDGVTRVSI 337
               SCOP domains d1qmha2 A:5-184,A:280-338 RNA 3'-terminal phosphate cyclase, RPTC                                                                                                                   d1qmha1 A:185-279 RNA 3'-terminal phosphate cyclase, RPTC, insert domain                       d1qmha2 A:5-184,A:280-338                                   SCOP domains
               CATH domains 1qmhA01 A:5-182,A:277-337  [code=3.65.10.20, no name defined]                                                                                                                     ---1qmhA02 A:186-276  [code=3.30.360.20, no name defined]                                     1qmhA01 A:5-182,A:277-337  [code=3.65.10.20, no name defined]- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhh..eee........eeee......eeeeeeee....hhhhhhhhhhhhh.....eeeeeee.........hhhhhhhhhhhhhhh..eeeeeeee........eeeeeeee...............eeeeeeeeeee..hhhhhhhhhhhhhhhh...eeeeeeehhhhh.eeeeeeeeee...eeeeeee.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh....eeee....eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------RTC        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qmh A   5 MIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSCHLLTNIAVVERFLPVRFSLIETDGVTRVSI 338
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334

Chain B from PDB  Type:PROTEIN  Length:335
 aligned with RTCA_ECOLI | P46849 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:335
                                    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     
           RTCA_ECOLI     4 MIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSCHLLTNIAVVERFLPVRFSLIETDGVTRVSIE 338
               SCOP domains d1qmhb2 B:5-184,B:280-339 RNA 3'-terminal phosphate cyclase, RPTC                                                                                                                   d1qmhb1 B:185-279 RNA 3'-terminal phosphate cyclase, RPTC, insert domain                       d1qmhb2 B:5-184,B:280-339                                    SCOP domains
               CATH domains 1qmhB01 B:5-182,B:277-337  [code=3.65.10.20, no name defined]                                                                                                                     ---1qmhB02 B:186-276  [code=3.30.360.20, no name defined]                                     1qmhB01 B:5-182,B:277-337  [code=3.65.10.20, no name defined]-- CATH domains
           Pfam domains (1) ---RTC-1qmhB01 B:8-329                                                                                                                                                                                                                                                                                                               ---------- Pfam domains (1)
           Pfam domains (2) ---RTC-1qmhB02 B:8-329                                                                                                                                                                                                                                                                                                               ---------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RTC_insert-1qmhB03 B:184-278                                                                   ------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RTC_insert-1qmhB04 B:184-278                                                                   ------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .eeee......hhhhhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhhh.eee........eeee.......eeeeeee....hhhhhhhhhhhhh.....eeeeeee..........hhhhhhhhhhhhhhh..eeeeeee........eeeeeee................eeeeeeeeeee..hhhhhhhhhhhhhhhh...eeeeeeehhhhh.eeeeeeeeee...eeeeeee.....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhh..eeeeee....eeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------RTC        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qmh B   5 MIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSCHLLTNIAVVERFLPVRFSLIETDGVTRVSIE 339
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334

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 '\|'

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EPT_RTPC (43)

Family: RTC (3)

Escherichia coli (strain K12) (2)

1a	RTC-1qmhB01	B:8-329
1b	RTC-1qmhB02	B:8-329

Clan: no clan defined [family: RTC_insert] (3)

Family: RTC_insert (3)

Escherichia coli (strain K12) (2)

2a	RTC_insert-1qmhB03	B:184-278
2b	RTC_insert-1qmhB04	B:184-278

Asymmetric/Biological 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.

Asymmetric/Biological Unit
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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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	RTCA_ECOLI \| P46849	:	1qmi 3kgd 3tut 3tux 3tv1 3tw3

1qmi	CRYSTAL STRUCTURE OF RNA 3'-TERMINAL PHOSPHATE CYCLASE, AN UBIQUITOUS ENZYME WITH UNUSUAL TOPOLOGY

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (1, 1)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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