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 5UX0 | pdb_00005ux0

X-ray crystal structure of Marinitoga piezophila Argonaute in complex with 5' OH guide RNA and target DNA

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
DSCOP2B SuperfamilyPAZ domain 8053684 3001750 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyRibonuclease H-like 8053686 3000143 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyMid domain of argonaute 8053685 3002210 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyRNA-binding domain, RBD 8053683 3000110 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyRNA-binding domain, RBD 8053683 3000110 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyRibonuclease H-like 8053686 3000143 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyPAZ domain 8053684 3001750 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyMid domain of argonaute 8053685 3002210 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
De5ux0D1 A: alpha arraysX: POZ domainH: POZ domainT: POZ domainF:ECOD (v295.2)
Ae5ux0A1 A: alpha arraysX: POZ domainH: POZ domainT: POZ domainF:ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, D
PF22136Bacterial argonaute protein N-terminal domain (MpAgo_N-like)Bacterial argonaute protein N-terminal domainArgonaute proteins are key effectors of eukaryotic RNA interference and, in prokaryotes, function in host genome defense. This entry represents a domain found at the N-terminus of the Marinitoga piezophila Argonaute (MpAgo) protein that uses 5'-hydr ...Argonaute proteins are key effectors of eukaryotic RNA interference and, in prokaryotes, function in host genome defense. This entry represents a domain found at the N-terminus of the Marinitoga piezophila Argonaute (MpAgo) protein that uses 5'-hydroxylated guide RNAs to recognise and cleave single-stranded target sequences rather than the 5'-phosphorylated guides used by all known Argonautes [1]. This domain adopts alpha/beta structure consisting of four-stranded beta-sheet and two helices. Compared to other Argonaute proteins, this domain differs in both its secondary structure and its orientation relative to the MID/PIWI lobe.
Domain
A, D
PF22362Argonaute, middle domain, bacteria (Ago_MID_bact)Argonaute, middle domain, bacteriaThis entry represents the middle domain of bacterial argonaute (Ago) [1,2]. Ago bind small RNA or DNA guides which provide base-pairing specificity for recognition and cleavage of complementary nucleic acid targets. Bacterial Ago adopt a bilobed stru ...This entry represents the middle domain of bacterial argonaute (Ago) [1,2]. Ago bind small RNA or DNA guides which provide base-pairing specificity for recognition and cleavage of complementary nucleic acid targets. Bacterial Ago adopt a bilobed structure; an N-terminal and a PAZ domain constitute one lobe, the second one consists of a middle (MID) domain and the catalytic PIWI domain. This domain mediates the recognition of the 5' end of the guide [1,2].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
C, F
DNA (5'-D(P*AP*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*CP*C)-3')---
B, E
RNA (5'-R(*G*GP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*AP*U)-3')---
A, D
Argonaute protein -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, D
IPR036397Ribonuclease H superfamilyHomologous Superfamily
A, D
IPR054387Argonaute, N-terminal domain, bacteriaDomain
A, D
IPR054434Argonaute, middle domain, bacteriaDomain
A, D
IPR003165Piwi domainDomain
A, D
IPR012337Ribonuclease H-like superfamilyHomologous Superfamily