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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

1ZBU

crystal structure of full-length 3'-exonuclease

Functional Information from GO Data
ChainGOidnamespacecontents
A0000175molecular_function3'-5'-RNA exonuclease activity
A0000460biological_processmaturation of 5.8S rRNA
A0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
A0003676molecular_functionnucleic acid binding
A0003723molecular_functionRNA binding
A0004518molecular_functionnuclease activity
A0004527molecular_functionexonuclease activity
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005730cellular_componentnucleolus
A0005737cellular_componentcytoplasm
A0006364biological_processrRNA processing
A0008408molecular_function3'-5' exonuclease activity
A0008859molecular_functionexoribonuclease II activity
A0016787molecular_functionhydrolase activity
A0019843molecular_functionrRNA binding
A0031047biological_processregulatory ncRNA-mediated gene silencing
A0031125biological_processrRNA 3'-end processing
A0043022molecular_functionribosome binding
A0046872molecular_functionmetal ion binding
A0060906biological_processnegative regulation of regulatory ncRNA-mediated heterochromatin formation
A0071044biological_processhistone mRNA catabolic process
A0071204cellular_componenthistone pre-mRNA 3'end processing complex
A0071207molecular_functionhistone pre-mRNA stem-loop binding
B0000175molecular_function3'-5'-RNA exonuclease activity
B0000460biological_processmaturation of 5.8S rRNA
B0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
B0003676molecular_functionnucleic acid binding
B0003723molecular_functionRNA binding
B0004518molecular_functionnuclease activity
B0004527molecular_functionexonuclease activity
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005730cellular_componentnucleolus
B0005737cellular_componentcytoplasm
B0006364biological_processrRNA processing
B0008408molecular_function3'-5' exonuclease activity
B0008859molecular_functionexoribonuclease II activity
B0016787molecular_functionhydrolase activity
B0019843molecular_functionrRNA binding
B0031047biological_processregulatory ncRNA-mediated gene silencing
B0031125biological_processrRNA 3'-end processing
B0043022molecular_functionribosome binding
B0046872molecular_functionmetal ion binding
B0060906biological_processnegative regulation of regulatory ncRNA-mediated heterochromatin formation
B0071044biological_processhistone mRNA catabolic process
B0071204cellular_componenthistone pre-mRNA 3'end processing complex
B0071207molecular_functionhistone pre-mRNA stem-loop binding
C0000175molecular_function3'-5'-RNA exonuclease activity
C0000460biological_processmaturation of 5.8S rRNA
C0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
C0003676molecular_functionnucleic acid binding
C0003723molecular_functionRNA binding
C0004518molecular_functionnuclease activity
C0004527molecular_functionexonuclease activity
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005730cellular_componentnucleolus
C0005737cellular_componentcytoplasm
C0006364biological_processrRNA processing
C0008408molecular_function3'-5' exonuclease activity
C0008859molecular_functionexoribonuclease II activity
C0016787molecular_functionhydrolase activity
C0019843molecular_functionrRNA binding
C0031047biological_processregulatory ncRNA-mediated gene silencing
C0031125biological_processrRNA 3'-end processing
C0043022molecular_functionribosome binding
C0046872molecular_functionmetal ion binding
C0060906biological_processnegative regulation of regulatory ncRNA-mediated heterochromatin formation
C0071044biological_processhistone mRNA catabolic process
C0071204cellular_componenthistone pre-mRNA 3'end processing complex
C0071207molecular_functionhistone pre-mRNA stem-loop binding
D0000175molecular_function3'-5'-RNA exonuclease activity
D0000460biological_processmaturation of 5.8S rRNA
D0000467biological_processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
D0003676molecular_functionnucleic acid binding
D0003723molecular_functionRNA binding
D0004518molecular_functionnuclease activity
D0004527molecular_functionexonuclease activity
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005730cellular_componentnucleolus
D0005737cellular_componentcytoplasm
D0006364biological_processrRNA processing
D0008408molecular_function3'-5' exonuclease activity
D0008859molecular_functionexoribonuclease II activity
D0016787molecular_functionhydrolase activity
D0019843molecular_functionrRNA binding
D0031047biological_processregulatory ncRNA-mediated gene silencing
D0031125biological_processrRNA 3'-end processing
D0043022molecular_functionribosome binding
D0046872molecular_functionmetal ion binding
D0060906biological_processnegative regulation of regulatory ncRNA-mediated heterochromatin formation
D0071044biological_processhistone mRNA catabolic process
D0071204cellular_componenthistone pre-mRNA 3'end processing complex
D0071207molecular_functionhistone pre-mRNA stem-loop binding
Functional Information from PDB Data
site_idAC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MG A 1000
ChainResidue
AASP134
AASP234
AMG1001
AAMP1002
site_idAC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG A 1001
ChainResidue
AAMP1002
AASP134
APHE135
AGLU136
AASP298
AMG1000
site_idAC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG B 2000
ChainResidue
BASP134
BPHE135
BASP234
BMG2001
BAMP2002
site_idAC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG B 2001
ChainResidue
BASP134
BGLU136
BASP298
BMG2000
BAMP2002
site_idAC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MG C 3000
ChainResidue
CASP134
CPHE135
CASP234
CAMP3002
site_idAC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MG C 3001
ChainResidue
CASP134
CGLU136
CASP298
CAMP3002
site_idAC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG D 4000
ChainResidue
DASP134
DASP230
DTRP233
DASP234
DMG4001
DAMP4002
site_idAC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG D 4001
ChainResidue
DASP134
DPHE135
DASP234
DMG4000
DAMP4002
site_idAC9
Number of Residues12
DetailsBINDING SITE FOR RESIDUE AMP A 1002
ChainResidue
AASP134
APHE135
AGLU136
AALA137
ATHR138
ACYS139
AASN143
APHE185
APHE238
AHIS293
AMG1000
AMG1001
site_idBC1
Number of Residues12
DetailsBINDING SITE FOR RESIDUE AMP B 2002
ChainResidue
BASP134
BPHE135
BGLU136
BALA137
BTHR138
BCYS139
BASN143
BPHE185
BPHE238
BHIS293
BMG2000
BMG2001
site_idBC2
Number of Residues12
DetailsBINDING SITE FOR RESIDUE AMP C 3002
ChainResidue
CASP134
CPHE135
CGLU136
CALA137
CTHR138
CCYS139
CASN143
CPHE185
CPHE238
CHIS293
CMG3000
CMG3001
site_idBC3
Number of Residues13
DetailsBINDING SITE FOR RESIDUE AMP D 4002
ChainResidue
DPHE135
DGLU136
DALA137
DTHR138
DCYS139
DASN143
DPHE185
DTHR190
DTRP233
DPHE238
DHIS293
DMG4000
DMG4001
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues8
DetailsActive site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"15451662","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1W0H","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues24
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"15451662","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1W0H","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
Catalytic Information from CSA
site_idMCSA1
Number of Residues5
DetailsM-CSA 784
ChainResidueDetails
AGLU146metal ligand
AVAL148electrostatic stabiliser, metal ligand, proton acceptor
ATYR250metal ligand
ALYS321electrostatic stabiliser, proton acceptor
AGLN326metal ligand
site_idMCSA2
Number of Residues5
DetailsM-CSA 784
ChainResidueDetails
BGLU146metal ligand
BVAL148electrostatic stabiliser, metal ligand, proton acceptor
BTYR250metal ligand
BLYS321electrostatic stabiliser, proton acceptor
BGLN326metal ligand
site_idMCSA3
Number of Residues5
DetailsM-CSA 784
ChainResidueDetails
CGLU146metal ligand
CVAL148electrostatic stabiliser, metal ligand, proton acceptor
CTYR250metal ligand
CLYS321electrostatic stabiliser, proton acceptor
CGLN326metal ligand
site_idMCSA4
Number of Residues5
DetailsM-CSA 784
ChainResidueDetails
DGLU146metal ligand
DVAL148electrostatic stabiliser, metal ligand, proton acceptor
DTYR250metal ligand
DLYS321electrostatic stabiliser, proton acceptor
DGLN326metal ligand

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PDB entries from 2025-12-24

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