6Y4Z | pdb_00006y4z

The crystal structure of human MACROD2 in space group P43212

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Utp12	e6y4zD1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Utp12	ECOD (v294.1)
C	Utp12	e6y4zC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Utp12	ECOD (v294.1)
B	Utp12	e6y4zB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Utp12	ECOD (v294.1)
A	Utp12	e6y4zA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Utp12	ECOD (v294.1)

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	Thioredoxin 1,ADP-ribose glycohydrolase MACROD2	deacetylase activity O-acetyl-ADP-ribose deacetylase activity hydrolase activity, acting on ester bonds deacylase activity carboxylic ester hydrolase activity hydrolase activity catalytic activity hydrolase activity, acting on glycosyl bonds ADP-ribosylglutamate hydrolase activity catalytic activity, acting on a protein hydrolase activity, hydrolyzing N-glycosyl compounds enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity deacetylase activity O-acetyl-ADP-ribose deacetylase activity hydrolase activity, acting on ester bonds deacylase activity carboxylic ester hydrolase activity hydrolase activity catalytic activity hydrolase activity, acting on glycosyl bonds ADP-ribosylglutamate hydrolase activity catalytic activity, acting on a protein hydrolase activity, hydrolyzing N-glycosyl compounds enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity molecular function activator activity molecular function regulator activity oxidoreductase activity, acting on a sulfur group of donors disulfide oxidoreductase activity oxidoreductase activity protein-disulfide reductase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development protein de-ADP-ribosylation peptidyl-glutamate ADP-deribosylation macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process biological process involved in interspecies interaction between organisms response to other organism response to bacterium response to external stimulus response to external biotic stimulus response to biotic stimulus nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process carbohydrate derivative metabolic process small molecule metabolic process purine nucleoside metabolic process nucleoside metabolic process purine-containing compound metabolic process cell redox homeostasis cellular homeostasis homeostatic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen nucleoplasm cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002589	Macro domain	Domain
A, B, C, D	IPR043472	Macro domain-like	Homologous Superfamily
A, B, C, D	IPR017937	Thioredoxin, conserved site	Conserved Site
A, B, C, D	IPR013766	Thioredoxin domain	Domain
A, B, C, D	IPR005746	Thioredoxin	Family
A, B, C, D	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: A1Z1Q3	liver cancer autism malignant ependymoma medulloblastoma Organic Mental Disorders, Substance-Induced pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia astrocytic tumor pituitary cancer atypical teratoid rhabdoid tumor psoriasis substance dependence interstitial cystitis malignant glioma non-small cell lung carcinoma osteosarcoma liver cancer autism malignant ependymoma medulloblastoma Organic Mental Disorders, Substance-Induced pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia astrocytic tumor pituitary cancer atypical teratoid rhabdoid tumor psoriasis substance dependence interstitial cystitis malignant glioma non-small cell lung carcinoma osteosarcoma Pick disease atopic eczema substance abuse B-cell chronic lymphocytic leukemia drug dependence tuberculosis glioblastoma Kabuki syndrome liver neoplasm malignant pancreatic neoplasm oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm pilocytic astrocytoma attention deficit hyperactivity disorder, inattentive type primitive neuroectodermal tumor autism spectrum disorder bipolar disorder substance-related disorder hypogonadotropic hypogonadism 21 with or without anosmia large cell medulloblastoma

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.