PDBsum entry 1uc2

Ligase

PDB id: 1uc2

Contents

Protein chains

480 a.a. *

Ligands

GLC-FRU ×2

SO4 ×9

Waters ×871

* Residue conservation analysis

PDB id:

1uc2

Name:

Ligase

Title:

Hypothetical extein protein of ph1602 from pyrococcus horikoshii

Structure:

Hypothetical protein ph1602. Chain: a, b. Synonym: ph1602. Engineered: yes

Source:

Pyrococcus horikoshii. Organism_taxid: 53953. Gene: ph1602_extein. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.15Å R-factor: 0.168 R-free: 0.204

Authors:

C.Okada,Y.Maegawa,M.Yao,I.Tanaka

Key ref:

C.Okada et al. (2006). Crystal structure of an RtcB homolog protein (PH1602-extein protein) from Pyrococcus horikoshii reveals a novel fold. Proteins, 63, 1119-1122. PubMed id: 16485279 DOI: 10.1002/prot.20912

Date:

08-Apr-03 Release date: 04-May-04

Protein chains

O59245  (RTCB_PYRHO) -  tRNA-splicing ligase RtcB from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

Seq: 871 a.a.

Struc: 480 a.a.*

* PDB and UniProt seqs differ at 88 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.3.1.-.-
• Enzyme class 2: E.C.6.5.1.8 - 3'-phosphate/5'-hydroxy nucleic acid ligase.
• Reaction:
  1. a 3'-end 3'-phospho-ribonucleotide-RNA + a 5'-end dephospho- ribonucleoside-RNA + GTP = a ribonucleotidyl-ribonucleotide-RNA + GMP + diphosphate
  2. a 3'-end 2',3'-cyclophospho-ribonucleotide-RNA + a 5'-end dephospho- ribonucleoside-RNA + GTP + H2O = a ribonucleotidyl-ribonucleotide-RNA + GMP + diphosphate + H⁺
• Cofactor: Mn(2+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1002/prot.20912

Proteins 63:1119-1122 (2006)

PubMed id: 16485279

Crystal structure of an RtcB homolog protein (PH1602-extein protein) from Pyrococcus horikoshii reveals a novel fold.

C.Okada, Y.Maegawa, M.Yao, I.Tanaka.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. a: Stereoview of monomeric PH1602-extein. -Helices are represented in cyan and three -sheets in yellow. The figure was prepared with MOLSCRIPT.[18] b: Schematic representation of the PH1602-extein topology, in the orientation of (a). The colors of helices and sheets are in accordance with (a). c: Electrostatic surface potential of the PH1602-extein (blue, positive potential; red, negative potential). The surface shows a positively charged cleft (black dashed line). A hydrophilic pocket exists in the center of the cleft (white circle). The figure was prepared with GRASP.[19] d: Same orientation as in (c). The surface consisting of conserved residues is colored green. The hydrophilic pocket is formed by conserved residues. The residues have been completely conserved in homologs from Pyrococcus horikoshii, Aeropyrum pernix, Sulfolobus solfataricus, Drosophila melanogaster, Homo sapiens, Caenorhabditis elegans, Nostoc sp, Escherichia coli, and Streptomyces avermitilis. The figure was prepared with PYMOL (DeLano Scientific).

The above figure is reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 63, 1119-1122) copyright 2006.