8J5T

Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the catalytic intermediate state

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: mpstruc

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00496	Bacterial extracellular solute-binding proteins, family 5 Middle (SBP_bac_5)	Bacterial extracellular solute-binding proteins, family 5 Middle	The borders of this family are based on the PDBSum definitions of the domain edges for Swiss:P06202.	Domain
B	PF00528	Binding-protein-dependent transport system inner membrane component (BPD_transp_1)	Binding-protein-dependent transport system inner membrane component	-	Family
B	PF19300	Binding-prot-dependent transport system membrane comp, N-term (BPD_transp_1_N)	Binding-prot-dependent transport system membrane comp, N-term	-	Family
C	PF00528	Binding-protein-dependent transport system inner membrane component (BPD_transp_1)	Binding-protein-dependent transport system inner membrane component	-	Family
C	PF12911	N-terminal TM domain of oligopeptide transport permease C (OppC_N)	N-terminal TM domain of oligopeptide transport permease C	Oligopeptide permeases (Opp) have been identified in numerous gram-negative and -positive bacteria. These transport systems belong to the superfamily of highly conserved ATP-binding cassette transporters. Typically, Opp importers comprise a complex o ...	Oligopeptide permeases (Opp) have been identified in numerous gram-negative and -positive bacteria. These transport systems belong to the superfamily of highly conserved ATP-binding cassette transporters. Typically, Opp importers comprise a complex of five proteins. The oligopeptide-binding protein OppA is responsible for the capture of peptides from the external medium. Two integral highly hydrophobic membrane spanning proteins, OppB and OppC, form a channel through the membrane used for peptide translocation. This N-terminal domain appears to be the first TM domain of the molecule [1].	Domain
D	PF08352	Oligopeptide/dipeptide transporter, C-terminal region (oligo_HPY)	Oligopeptide/dipeptide transporter, C-terminal region	-	Family
D	PF00005	ABC transporter (ABC_tran)	ABC transporter	ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are comp ...	ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain Pfam:PF00664. These four domains may belong to a single polypeptide as in Swiss:P13569, or belong in different polypeptide chains.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Uncharacterized protein Rv1280c	binding peptide binding peptide transmembrane transporter activity transporter activity transmembrane transporter activity amide binding modified amino acid binding ion binding oligopeptide binding anion binding glutathione binding sulfur compound binding small molecule binding	protein localization protein import establishment of protein localization cellular localization nitrogen compound transport transport establishment of localization localization protein transport cellular macromolecule localization macromolecule localization cellular process peptide transport amide transport	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex cellular anatomical entity transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex periplasmic space outer membrane-bounded periplasmic space cell envelope
B	Putative peptide transport permease protein Rv1283c	-	peptide transport localization nitrogen compound transport amide transport transport establishment of localization transmembrane transport cellular process protein localization establishment of protein localization cellular localization protein transport cellular macromolecule localization macromolecule localization	cell periphery plasma membrane membrane cellular anatomical entity
C	Putative peptide transport permease protein Rv1282c	-	peptide transport localization nitrogen compound transport amide transport transport establishment of localization transmembrane transport cellular process protein localization establishment of protein localization cellular localization protein transport cellular macromolecule localization macromolecule localization	cell periphery plasma membrane membrane cellular anatomical entity
D	Uncharacterized ABC transporter ATP-binding protein Rv1281c	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity ATP hydrolysis 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 ATP-dependent activity transporter activity transmembrane transporter activity	peptide transport localization nitrogen compound transport amide transport transport establishment of localization transmembrane transport cellular process	cell periphery plasma membrane membrane cellular anatomical entity external encapsulating structure cell wall peptidoglycan-based cell wall

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000914	Solute-binding protein family 5 domain	Domain
A	IPR039424	Solute-binding protein family 5	Family
A	IPR030678	Peptide/nickel binding protein, MppA-type	Family
B	IPR000515	ABC transporter type 1, transmembrane domain MetI-like	Domain
B	IPR035906	MetI-like superfamily	Homologous Superfamily
B	IPR045621	ABC transporter type 1, GsiC-like, N-terminal domain	Domain
C	IPR025966	Oligopeptide transport permease C-like, N-terminal domain	Domain
C	IPR000515	ABC transporter type 1, transmembrane domain MetI-like	Domain
C	IPR035906	MetI-like superfamily	Homologous Superfamily
D	IPR003593	AAA+ ATPase domain	Domain
D	IPR017871	ABC transporter-like, conserved site	Conserved Site
D	IPR013563	Oligopeptide/dipeptide ABC transporter, C-terminal	Domain
D	IPR003439	ABC transporter-like, ATP-binding domain	Domain
D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	ATP Binding Cassette (ABC) Transporters	OppABCD oligopeptide permease in pre-translocation state

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.