1ZBU
crystal structure of full-length 3'-exonuclease
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000175 | molecular_function | 3'-5'-RNA exonuclease activity |
| A | 0000460 | biological_process | maturation of 5.8S rRNA |
| A | 0000467 | biological_process | exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) |
| A | 0003676 | molecular_function | nucleic acid binding |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005730 | cellular_component | nucleolus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0006364 | biological_process | rRNA processing |
| A | 0008408 | molecular_function | 3'-5' exonuclease activity |
| A | 0008859 | molecular_function | exoribonuclease II activity |
| A | 0019843 | molecular_function | rRNA binding |
| A | 0031125 | biological_process | rRNA 3'-end processing |
| A | 0043022 | molecular_function | ribosome binding |
| A | 0060906 | biological_process | negative regulation of regulatory ncRNA-mediated heterochromatin formation |
| A | 0071044 | biological_process | histone mRNA catabolic process |
| A | 0071204 | cellular_component | histone pre-mRNA 3'end processing complex |
| A | 0071207 | molecular_function | histone pre-mRNA stem-loop binding |
| B | 0000175 | molecular_function | 3'-5'-RNA exonuclease activity |
| B | 0000460 | biological_process | maturation of 5.8S rRNA |
| B | 0000467 | biological_process | exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) |
| B | 0003676 | molecular_function | nucleic acid binding |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005730 | cellular_component | nucleolus |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0006364 | biological_process | rRNA processing |
| B | 0008408 | molecular_function | 3'-5' exonuclease activity |
| B | 0008859 | molecular_function | exoribonuclease II activity |
| B | 0019843 | molecular_function | rRNA binding |
| B | 0031125 | biological_process | rRNA 3'-end processing |
| B | 0043022 | molecular_function | ribosome binding |
| B | 0060906 | biological_process | negative regulation of regulatory ncRNA-mediated heterochromatin formation |
| B | 0071044 | biological_process | histone mRNA catabolic process |
| B | 0071204 | cellular_component | histone pre-mRNA 3'end processing complex |
| B | 0071207 | molecular_function | histone pre-mRNA stem-loop binding |
| C | 0000175 | molecular_function | 3'-5'-RNA exonuclease activity |
| C | 0000460 | biological_process | maturation of 5.8S rRNA |
| C | 0000467 | biological_process | exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) |
| C | 0003676 | molecular_function | nucleic acid binding |
| C | 0005515 | molecular_function | protein binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005730 | cellular_component | nucleolus |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0006364 | biological_process | rRNA processing |
| C | 0008408 | molecular_function | 3'-5' exonuclease activity |
| C | 0008859 | molecular_function | exoribonuclease II activity |
| C | 0019843 | molecular_function | rRNA binding |
| C | 0031125 | biological_process | rRNA 3'-end processing |
| C | 0043022 | molecular_function | ribosome binding |
| C | 0060906 | biological_process | negative regulation of regulatory ncRNA-mediated heterochromatin formation |
| C | 0071044 | biological_process | histone mRNA catabolic process |
| C | 0071204 | cellular_component | histone pre-mRNA 3'end processing complex |
| C | 0071207 | molecular_function | histone pre-mRNA stem-loop binding |
| D | 0000175 | molecular_function | 3'-5'-RNA exonuclease activity |
| D | 0000460 | biological_process | maturation of 5.8S rRNA |
| D | 0000467 | biological_process | exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) |
| D | 0003676 | molecular_function | nucleic acid binding |
| D | 0005515 | molecular_function | protein binding |
| D | 0005634 | cellular_component | nucleus |
| D | 0005730 | cellular_component | nucleolus |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0006364 | biological_process | rRNA processing |
| D | 0008408 | molecular_function | 3'-5' exonuclease activity |
| D | 0008859 | molecular_function | exoribonuclease II activity |
| D | 0019843 | molecular_function | rRNA binding |
| D | 0031125 | biological_process | rRNA 3'-end processing |
| D | 0043022 | molecular_function | ribosome binding |
| D | 0060906 | biological_process | negative regulation of regulatory ncRNA-mediated heterochromatin formation |
| D | 0071044 | biological_process | histone mRNA catabolic process |
| D | 0071204 | cellular_component | histone pre-mRNA 3'end processing complex |
| D | 0071207 | molecular_function | histone pre-mRNA stem-loop binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG A 1000 |
| Chain | Residue |
| A | ASP134 |
| A | ASP234 |
| A | MG1001 |
| A | AMP1002 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG A 1001 |
| Chain | Residue |
| A | AMP1002 |
| A | ASP134 |
| A | PHE135 |
| A | GLU136 |
| A | ASP298 |
| A | MG1000 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG B 2000 |
| Chain | Residue |
| B | ASP134 |
| B | PHE135 |
| B | ASP234 |
| B | MG2001 |
| B | AMP2002 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG B 2001 |
| Chain | Residue |
| B | ASP134 |
| B | GLU136 |
| B | ASP298 |
| B | MG2000 |
| B | AMP2002 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG C 3000 |
| Chain | Residue |
| C | ASP134 |
| C | PHE135 |
| C | ASP234 |
| C | AMP3002 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG C 3001 |
| Chain | Residue |
| C | ASP134 |
| C | GLU136 |
| C | ASP298 |
| C | AMP3002 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG D 4000 |
| Chain | Residue |
| D | ASP134 |
| D | ASP230 |
| D | TRP233 |
| D | ASP234 |
| D | MG4001 |
| D | AMP4002 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG D 4001 |
| Chain | Residue |
| D | ASP134 |
| D | PHE135 |
| D | ASP234 |
| D | MG4000 |
| D | AMP4002 |
| site_id | AC9 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE AMP A 1002 |
| Chain | Residue |
| A | ASP134 |
| A | PHE135 |
| A | GLU136 |
| A | ALA137 |
| A | THR138 |
| A | CYS139 |
| A | ASN143 |
| A | PHE185 |
| A | PHE238 |
| A | HIS293 |
| A | MG1000 |
| A | MG1001 |
| site_id | BC1 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE AMP B 2002 |
| Chain | Residue |
| B | ASP134 |
| B | PHE135 |
| B | GLU136 |
| B | ALA137 |
| B | THR138 |
| B | CYS139 |
| B | ASN143 |
| B | PHE185 |
| B | PHE238 |
| B | HIS293 |
| B | MG2000 |
| B | MG2001 |
| site_id | BC2 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE AMP C 3002 |
| Chain | Residue |
| C | ASP134 |
| C | PHE135 |
| C | GLU136 |
| C | ALA137 |
| C | THR138 |
| C | CYS139 |
| C | ASN143 |
| C | PHE185 |
| C | PHE238 |
| C | HIS293 |
| C | MG3000 |
| C | MG3001 |
| site_id | BC3 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE AMP D 4002 |
| Chain | Residue |
| D | PHE135 |
| D | GLU136 |
| D | ALA137 |
| D | THR138 |
| D | CYS139 |
| D | ASN143 |
| D | PHE185 |
| D | THR190 |
| D | TRP233 |
| D | PHE238 |
| D | HIS293 |
| D | MG4000 |
| D | MG4001 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 8 |
| Details | Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"15451662","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1W0H","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 24 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"15451662","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1W0H","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 5 |
| Details | M-CSA 784 |
| Chain | Residue | Details |
| A | GLU146 | metal ligand |
| A | VAL148 | electrostatic stabiliser, metal ligand, proton acceptor |
| A | TYR250 | metal ligand |
| A | LYS321 | electrostatic stabiliser, proton acceptor |
| A | GLN326 | metal ligand |
| site_id | MCSA2 |
| Number of Residues | 5 |
| Details | M-CSA 784 |
| Chain | Residue | Details |
| B | GLU146 | metal ligand |
| B | VAL148 | electrostatic stabiliser, metal ligand, proton acceptor |
| B | TYR250 | metal ligand |
| B | LYS321 | electrostatic stabiliser, proton acceptor |
| B | GLN326 | metal ligand |
| site_id | MCSA3 |
| Number of Residues | 5 |
| Details | M-CSA 784 |
| Chain | Residue | Details |
| C | GLU146 | metal ligand |
| C | VAL148 | electrostatic stabiliser, metal ligand, proton acceptor |
| C | TYR250 | metal ligand |
| C | LYS321 | electrostatic stabiliser, proton acceptor |
| C | GLN326 | metal ligand |
| site_id | MCSA4 |
| Number of Residues | 5 |
| Details | M-CSA 784 |
| Chain | Residue | Details |
| D | GLU146 | metal ligand |
| D | VAL148 | electrostatic stabiliser, metal ligand, proton acceptor |
| D | TYR250 | metal ligand |
| D | LYS321 | electrostatic stabiliser, proton acceptor |
| D | GLN326 | metal ligand |
