DB code: D00302

RLCP classification 3.133.305000.384 : Transfer
3.103.90000.335 : Transfer
CATH domain 3.65.10.20 : UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain Catalytic domain
3.30.360.20 : Dihydrodipicolinate Reductase; domain 2
E.C. 6.5.1.4
CSA 1qmh
M-CSA 1qmh
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P46849 RNA 3''-terminal phosphate cyclase
RNA-3''-phosphate cyclase
RNA cyclase
EC 6.5.1.4
YP_026219.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_492013.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF01137 (RTC)
PF05189 (RTC_insert)
[Graphical View]

KEGG enzyme name
RNA-3'-phosphate cyclase
RNA cyclase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P46849 RTCA_ECOLI ATP + RNA 3''-terminal-phosphate = AMP + diphosphate + RNA terminal-2'',3''-cyclic-phosphate. Homodimer, disulfide-linked. Cytoplasm.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00002 C03638 C00013 C00020 C04312
E.C.
Compound Magnesium ATP RNA 3'-terminal-phosphate Pyrophosphate AMP RNA terminal-2',3'-cyclic-phosphate
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide nucleic acids phosphate group/phosphate ion amine group,nucleotide nucleic acids
ChEBI 18420
15422
29888
16027
PubChem 888
5957
1023
21961011
6083
1qmhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:CIT Unbound Unbound Unbound
1qmhB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:CIT Unbound Unbound Unbound
1qmiA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1qmiB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1qmiC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1qmiD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1qmhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1qmhB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1qmiA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1qmiB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1qmiC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1qmiD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [7]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1qmhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 14;GLN 18;ARG 21;ARG 40;ARG 43;GLN 51;HIS 52;HIS 309 GLY 17
1qmhB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 14;GLN 18;ARG 21;ARG 40;ARG 43;GLN 51;HIS 52;HIS 309 GLY 17
1qmiA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 14;GLN 18;ARG 21;ARG 40;ARG 43;GLN 51;HIS 52;HIS 309 GLY 17
1qmiB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 14;GLN 18;ARG 21;ARG 40;ARG 43;GLN 51;HIS 52;HIS 309 GLY 17
1qmiC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 14;GLN 18;ARG 21;ARG 40;ARG 43;GLN 51;HIS 52;HIS 309 GLY 17
1qmiD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 14;GLN 18;ARG 21;ARG 40;ARG 43;GLN 51;HIS 52;HIS 309 GLY 17
1qmhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qmhB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qmiA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qmiB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qmiC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qmiD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
[5]
[7]

References
[1]
Resource
Comments
Medline ID
PubMed ID 2579395
Journal Proc Natl Acad Sci U S A
Year 1985
Volume 82
Pages 1316-20
Authors Filipowicz W, Strugala K, Konarska M, Shatkin AJ
Title Cyclization of RNA 3'-terminal phosphate by cyclase from HeLa cells proceeds via formation of N(3')pp(5')A activated intermediate.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 2199762
Journal Methods Enzymol
Year 1990
Volume 181
Pages 499-510
Authors Filipowicz W, Vicente O
Title RNA 3'-terminal phosphate cyclase from HeLa cells.
Related PDB
Related UniProtKB
[3]
Resource
Comments REVISION, AND CHARACTERIZATION
Medline ID 97327572
PubMed ID 9184239
Journal EMBO J
Year 1997
Volume 16
Pages 2955-67
Authors Genschik P, Billy E, Swianiewicz M, Filipowicz W
Title The human RNA 3'-terminal phosphate cyclase is a member of a new family of proteins conserved in Eucarya, Bacteria and Archaea.
Related PDB
Related UniProtKB P46849
[4]
Resource
Comments
Medline ID
PubMed ID 10397337
Journal Acta Biochim Pol
Year 1998
Volume 45
Pages 895-906
Authors Filipowicz W, Billy E, Drabikowski K, Genschik P
Title Cyclases of the 3'-terminal phosphate in RNA: a new family of RNA processing enzymes conserved in eucarya, bacteria and archaea.
Related PDB
Related UniProtKB
[5]
Resource
Comments CHARACTERIZATION
Medline ID 98411361
PubMed ID 9738023
Journal J Biol Chem
Year 1998
Volume 273
Pages 25516-26
Authors Genschik P, Drabikowski K, Filipowicz W
Title Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase and its sigma54-regulated operon.
Related PDB
Related UniProtKB P46849
[6]
Resource
Comments
Medline ID
PubMed ID 10574971
Journal J Biol Chem
Year 1999
Volume 274
Pages 34955-60
Authors Billy E, Hess D, Hofsteenge J, Filipowicz W
Title Characterization of the adenylation site in the RNA 3'-terminal phosphate cyclase from Escherichia coli.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS)
Medline ID 20139688
PubMed ID 10673421
Journal Structure Fold Des
Year 2000
Volume 8
Pages 13-23
Authors Palm GJ, Billy E, Filipowicz W, Wlodawer A
Title Crystal structure of RNA 3'-terminal phosphate cyclase, a ubiquitous enzyme with unusual topology.
Related PDB 1qmh 1qmi
Related UniProtKB P46849

Comments
This enzyme catalyzes two successive transfer reactions, an AMP transfer and an intramolecular phosphoryl transfer. Although the detailed mechanism remains unclear, the reactions may proceed in the following way (see [1], [3] & [7]).
(A) The AMP transfer reaction proceeds through an adenylated-enzyme intermediate.
(1) His309 makes a nucleophilic attack on the gamma-phosphate of ATP (the first substrate), to form an adenylated histidine residue as an intermediate, releasing pyrophosphate (originally, gamma- and beta-phosphate groups of ATP) as a leaving group. Here, Glu14 probably activates His309 by acting as a general base to abstract proton from the residue, considering the active-site structure (see [7]). During the reaction, cofactor magnesium ion and Arginine/Histidine/Glutamine cluster and main chain (composed of Gly17, Gln18, Arg21, Arg40, Arg43 and His52) stabilize the transition state.
(2) As the acceptor group, 3'-terminal phosphate of the second substrate, RNA, makes a nucleophilic attack on the phosphoryl group of the adenylated histidine, to form the second intermediate, RNA-N(3')pp(5')A.
(B) The intramolecular phosphoryl transfer to 2'-OH may occur spontaneously (see [3]).
(1') The adjacent 2'-OH group, as the second acceptor group, makes a nucleophilic attack on the phosphorus atom in the phosphodiester linkage, releasing AMP as a leaving group. During this reaction, cofactor magnesium ion and Arginine/Histidine/Glutamine cluster and main chain (composed of Gly17, Gln18, Arg21, Arg40, Arg43 and His52) may also stabilize the transition state.
As magnesium ion binding site has not been elucidated yet, it might be bound directly to the phosphate groups of ATP or AMP.

Created Updated
2004-10-22 2009-02-26