5IIT | pdb_00005iit

Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Macro domain-like	8036145	3000458	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Macro domain-like	8036145	3000458	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Macro domain-like	8036145	3000458	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Macro domain-like	8036145	3000458	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	SPX	e5iitD2	A: alpha bundles	X: SPX domain (From Topology)	H: SPX domain (From Topology)	T: SPX domain	F: SPX	ECOD (1.6)
D	Macro	e5iitD1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
A	SPX	e5iitA2	A: alpha bundles	X: SPX domain (From Topology)	H: SPX domain (From Topology)	T: SPX domain	F: SPX	ECOD (1.6)
A	Macro	e5iitA1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
B	SPX	e5iitB2	A: alpha bundles	X: SPX domain (From Topology)	H: SPX domain (From Topology)	T: SPX domain	F: SPX	ECOD (1.6)
B	Macro	e5iitB1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
C	SPX	e5iitC2	A: alpha bundles	X: SPX domain (From Topology)	H: SPX domain (From Topology)	T: SPX domain	F: SPX	ECOD (1.6)
C	Macro	e5iitC1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (utative)
A	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (utative)
B	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (utative)
C	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01661	Macro domain (Macro)	Macro domain	The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent [1]: in certain cases it is believed to bind non-covalently ...	The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent [1]: in certain cases it is believed to bind non-covalently [2]; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein [3]. This domain is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein 4 and also in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alpha-viruses and coronaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria and eukaryotes. The 3D structure of the SARS-CoV Macro domain has a mixed alpha/beta fold consisting of a central seven-stranded twisted mixed beta sheet sandwiched between two alpha helices on one face, and three on the other. The final alpha-helix, located on the edge of the central beta-sheet, forms the C terminus of the protein [4]. The crystal structure of AF1521 (a Macro domain-only protein from Archaeoglobus fulgidus) has also been reported and compared with other Macro domain containing proteins. Several Macro domain only proteins are shorter than AF1521, and appear to lack either the first strand of the beta-sheet or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Vacuolar transporter chaperone 4,Core histone macro-H2A.1	kinase activity transferase activity polyphosphate kinase activity catalytic activity phosphotransferase activity, phosphate group as acceptor transferase activity, transferring phosphorus-containing groups protein binding binding calmodulin binding ion binding inositol hexakisphosphate binding alcohol binding anion binding small molecule binding kinase activity transferase activity polyphosphate kinase activity catalytic activity phosphotransferase activity, phosphate group as acceptor transferase activity, transferring phosphorus-containing groups protein binding binding calmodulin binding ion binding inositol hexakisphosphate binding alcohol binding anion binding small molecule binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding nucleoside phosphate binding ADP-D-ribose binding heterocyclic compound binding carbohydrate derivative binding chromatin binding promoter-specific chromatin binding rDNA binding double-stranded methylated DNA binding protein heterodimerization activity protein dimerization activity structural molecule activity structural constituent of chromatin RNA polymerase II transcription regulatory region sequence-specific DNA binding kinase binding enzyme binding protein kinase binding chromatin DNA binding ADP-D-ribose modification-dependent protein binding poly-ADP-D-ribose modification-dependent protein binding modification-dependent protein binding protein-containing complex binding nucleosome binding nucleosomal DNA binding protein serine/threonine kinase activity enzyme regulator activity catalytic activity, acting on a protein protein kinase activity enzyme inhibitor activity protein kinase regulator activity phosphotransferase activity, alcohol group as acceptor protein kinase inhibitor activity molecular function inhibitor activity molecular function regulator activity protein serine/threonine kinase inhibitor activity kinase inhibitor activity kinase regulator activity	localization cellular localization transport establishment of localization in cell vacuolar transport intracellular transport cellular process establishment of localization catabolic process autophagy microautophagy metabolic process process utilizing autophagic mechanism membrane organization localization cellular localization transport establishment of localization in cell vacuolar transport intracellular transport cellular process establishment of localization catabolic process autophagy microautophagy metabolic process process utilizing autophagic mechanism membrane organization engulfment of target by autophagosome autophagosome assembly organelle assembly vacuole organization macroautophagy autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly membrane invagination cellular component organization or biogenesis biosynthetic process polyphosphate biosynthetic process oxoacid metabolic process small molecule metabolic process organic acid metabolic process phosphorus metabolic process polyphosphate metabolic process response to oxidative stress regulation of biological process response to stimulus regulation of response to stimulus response to stress regulation of response to stress regulation of response to oxidative stress biological regulation regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process epigenetic regulation of gene expression primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of gene expression positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process negative regulation of response to stimulus negative regulation of biological process negative regulation of response to oxidative stress aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds regulation of generation of precursor metabolites and energy generation of precursor metabolites and energy regulation of cellular respiration regulation of aerobic respiration regulation of oxidative phosphorylation sex-chromosome dosage compensation cellular response to stimulus DNA metabolic process cellular response to stress DNA damage response DNA repair regulation of primary metabolic process negative regulation of RNA biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process negative regulation of transcription of nucleolar large rRNA by RNA polymerase I regulation of transcription of nucleolar large rRNA by RNA polymerase I negative regulation of transcription by RNA polymerase I transcription by RNA polymerase I rRNA transcription rRNA metabolic process regulation of transcription by RNA polymerase I nucleolar large rRNA transcription by RNA polymerase I cell cycle G2/M phase transition regulation of cell cycle phase transition regulation of cell cycle process negative regulation of cell cycle regulation of cell cycle G2/M phase transition cell cycle phase transition negative regulation of cell cycle process negative regulation of cell cycle G2/M phase transition negative regulation of cell cycle phase transition cell cycle regulation of cell cycle cell cycle process regulation of lipid metabolic process lipid metabolic process regulation of NAD metabolic process NAD metabolic process purine nucleotide metabolic process regulation of small molecule metabolic process nucleobase-containing small molecule metabolic process regulation of nucleotide metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process pyridine nucleotide metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process regulation of purine nucleotide metabolic process nucleotide metabolic process purine-containing compound metabolic process organophosphate metabolic process regulation of phosphorus metabolic process regulation of maintenance of mitotic sister chromatid cohesion positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization mitotic sister chromatid cohesion maintenance of sister chromatid cohesion maintenance of mitotic sister chromatid cohesion positive regulation of cell cycle process chromosome organization sister chromatid cohesion regulation of chromosome organization positive regulation of maintenance of sister chromatid cohesion positive regulation of maintenance of mitotic sister chromatid cohesion positive regulation of sister chromatid cohesion regulation of organelle organization positive regulation of cell cycle positive regulation of chromosome organization regulation of maintenance of sister chromatid cohesion regulation of sister chromatid cohesion positive regulation of response to oxidative stress positive regulation of response to stimulus protein localization regulation of localization regulation of protein localization negative regulation of protein localization to chromosome, telomeric region protein localization to chromosome, telomeric region regulation of protein localization to chromosome, telomeric region protein localization to chromosome regulation of cellular localization cellular macromolecule localization macromolecule localization protein localization to organelle negative regulation of protein localization negative regulation of gene expression negative regulation of gene expression, epigenetic protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization protein-containing complex assembly nucleosome assembly nucleosome organization multicellular organismal process regulation of developmental process cellular developmental process regulation of cell differentiation embryo development positive regulation of developmental process multicellular organism development positive regulation of cell differentiation regulation of endodermal cell differentiation cell differentiation anatomical structure development developmental process formation of primary germ layer embryonic morphogenesis positive regulation of endodermal cell differentiation tissue development gastrulation anatomical structure morphogenesis endoderm development anatomical structure formation involved in morphogenesis endoderm formation endodermal cell differentiation regulation of protein modification process regulation of catalytic activity regulation of protein phosphorylation negative regulation of phosphate metabolic process negative regulation of catalytic activity regulation of transferase activity negative regulation of kinase activity negative regulation of transferase activity negative regulation of protein serine/threonine kinase activity negative regulation of protein modification process protein metabolic process protein modification process negative regulation of protein metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process negative regulation of molecular function negative regulation of protein kinase activity regulation of protein kinase activity regulation of molecular function regulation of kinase activity negative regulation of protein phosphorylation macromolecule modification regulation of protein serine/threonine kinase activity negative regulation of phosphorus metabolic process regulation of phosphorylation negative regulation of phosphorylation heterochromatin formation positive regulation of keratinocyte differentiation regulation of epidermal cell differentiation epidermis development epithelial cell differentiation regulation of epithelial cell differentiation regulation of multicellular organismal process epithelium development regulation of multicellular organismal development epidermal cell differentiation animal organ development positive regulation of epidermis development positive regulation of epithelial cell differentiation skin development keratinocyte differentiation positive regulation of multicellular organismal process regulation of epidermis development regulation of keratinocyte differentiation positive regulation of epidermal cell differentiation establishment of protein localization protein localization to chromatin establishment of protein localization to chromatin establishment of protein localization to organelle establishment of protein localization to chromosome	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle vacuolar membrane storage vacuole membrane lytic vacuole membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle vacuolar membrane storage vacuole membrane lytic vacuole vacuole fungal-type vacuole lytic vacuole membrane bounding membrane of organelle organelle membrane fungal-type vacuole membrane autophagosome membrane autophagosome cell periphery cell cortex protein-containing complex vacuolar transporter chaperone complex membrane protein complex intracellular protein-containing complex endoplasmic reticulum endomembrane system organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle membraneless organelle intracellular membraneless organelle chromatin chromosome nucleus membrane-enclosed lumen nuclear chromosome intracellular organelle lumen organelle lumen nuclear lumen chromosome, telomeric region chromosomal region nucleolus condensed chromosome sex chromosome heterochromatin sex chromatin protein-DNA complex nucleosome Barr body X chromosome nucleoplasm pericentric heterochromatin chromosome, centromeric region site of DNA damage

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR042267	VTC domain superfamily	Homologous Superfamily
A, B, C, D	IPR003807	Domain of unknown function DUF202	Domain
A, B, C, D	IPR004331	SPX domain	Domain
A, B, C, D	IPR018966	VTC domain	Domain
A, B, C, D	IPR051572	Vacuolar Transporter Chaperone Complex Subunit	Family
A, B, C, D	IPR035796	Core histone macro-H2A, macro domain	Domain
A, B, C, D	IPR032454	Histone H2A, C-terminal domain	Domain
A, B, C, D	IPR007125	Histone H2A/H2B/H3	Domain
A, B, C, D	IPR002119	Histone H2A	Family
A, B, C, D	IPR021171	Core histone macro-H2A	Family
A, B, C, D	IPR009072	Histone-fold	Homologous Superfamily
A, B, C, D	IPR002589	Macro domain	Domain
A, B, C, D	IPR043472	Macro domain-like	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: O75367	pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis acute myeloid leukemia ductal breast carcinoma in situ IgA glomerulonephritis lung adenocarcinoma malignant mesothelioma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma Pick disease rheumatoid arthritis adenoma esophageal adenocarcinoma invasive ductal breast carcinoma lung cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis acute myeloid leukemia ductal breast carcinoma in situ IgA glomerulonephritis lung adenocarcinoma malignant mesothelioma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma Pick disease rheumatoid arthritis adenoma esophageal adenocarcinoma invasive ductal breast carcinoma lung cancer medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm plasma cell myeloma tuberculosis astrocytic tumor glioblastoma large cell medulloblastoma lymphoplasmacytic lymphoma myopathy pancreatic ductal adenocarcinoma

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 R01GM157729.