3MMP | pdb_00003mmp

Structure of the Qb replicase, an RNA-dependent RNA polymerase consisting of viral and host proteins

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	EF-Tu post-G domain-like	8056531	3002024	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Elongation factor Ts (EF-Ts), dimerisation domain	8032444	3000908	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Elongation factor Ts (EF-Ts), dimerisation domain	8035038	3000908	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EF-Tu post-G domain-like	8056533	3002024	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8056530	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	UBA-like	8032443	3001235	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Elongation factor Ts (EF-Ts), dimerisation domain	8035038	3000908	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-Tu post-G domain-like	8056531	3002024	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-Tu post-G domain-like	8056533	3002024	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	UBA-like	8032443	3001235	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Elongation factor Ts (EF-Ts), dimerisation domain	8032444	3000908	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8056530	3002022	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth F]	CBM32	e3mmpF1	A: alpha bundles	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: CBM32	ECOD (develop294)
B [auth G]	RNA_replicase_B	e3mmpG1	A: alpha bundles	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: RNA_replicase_B	ECOD (develop294)
B [auth G]	CBM32	e3mmpG2	A: alpha bundles	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: CBM32	ECOD (develop294)
C		e3mmpC7	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F:	ECOD (develop294)
C	RhaA	e3mmpC2	A: alpha bundles	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: RhaA	ECOD (develop294)
A	RA	e3mmpA2	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: RA	ECOD (develop294)
A	RhaA	e3mmpA3	A: alpha bundles	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: RhaA	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
A	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00009	Elongation factor Tu GTP binding domain (GTP_EFTU)	Elongation factor Tu GTP binding domain	This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.	Domain
A, C	PF00889	Elongation factor TS (EF_TS)	Elongation factor TS	-	Family
A, C	PF03143	Elongation factor Tu C-terminal domain (GTP_EFTU_D3)	Elongation factor Tu C-terminal domain	Elongation factor Tu consists of three structural domains, this is the third domain. This domain adopts a beta barrel structure. This the third domain is involved in binding to both charged tRNA [1] and binding to EF-Ts Pfam:PF00889 [2].	Domain
A, C	PF03144	Elongation factor Tu domain 2 (GTP_EFTU_D2)	Elongation factor Tu domain 2	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as e ...	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to Pfam:PF03143, and in fact has weak sequence matches to this domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth G], D [auth F]	RNA-directed RNA polymerase beta chain	RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups RNA binding binding nucleic acid binding nucleoside phosphate binding nucleotide binding RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups RNA binding binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding	RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process	-
A, C	Elongation factor Tu 2, Elongation factor Ts	translation factor activity translation elongation factor activity GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding translation factor activity translation elongation factor activity GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding magnesium ion binding guanosine tetraphosphate binding guanyl nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding RNA binding nucleic acid binding GTP binding purine ribonucleoside triphosphate binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	primary metabolic process translation gene expression macromolecule biosynthetic process protein biosynthetic process biosynthetic process translational elongation metabolic process cellular process macromolecule metabolic process protein metabolic process response to stimulus response to chemical response to antibiotic	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol protein-containing complex guanyl-nucleotide exchange factor complex intracellular protein-containing complex cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth G], D [auth F]	IPR007096	RNA-directed RNA polymerase, catalytic domain, bacteriophage	Domain
B [auth G], D [auth F]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
B [auth G], D [auth F]	IPR005093	RNA-directed RNA polymerase beta-chain	Family
A, C	IPR014039	Translation elongation factor EFTs/EF1B, dimerisation	Domain
A, C	IPR018101	Translation elongation factor Ts, conserved site	Conserved Site
A, C	IPR001816	Translation elongation factor EFTs/EF1B	Family
A, C	IPR036402	Elongation factor Ts, dimerisation domain superfamily	Homologous Superfamily
A, C	IPR009060	UBA-like superfamily	Homologous Superfamily
A, C	IPR005225	Small GTP-binding domain	Domain
A, C	IPR000795	Translational (tr)-type GTP-binding domain	Domain
A, C	IPR033720	Elongation factor Tu, domain 2	Domain
A, C	IPR009001	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal	Homologous Superfamily
A, C	IPR031157	Tr-type G domain, conserved site	Conserved Site
A, C	IPR004541	Translation elongation factor EFTu/EF1A, bacterial/organelle	Family
A, C	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
A, C	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A, C	IPR004160	Translation elongation factor EFTu/EF1A, C-terminal	Domain
A, C	IPR050055	Elongation factor Tu GTPase	Family
A, C	IPR041709	Elongation factor Tu (EF-Tu), GTP-binding domain	Domain
A, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily