PHM/PNGase F superfamily

SCOP classification

• Root: SCOP hierarchy in SUPERFAMILY [ 0] (11)
• Class: All beta proteins [ 48724] (174)
• Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) [ 88632] (7)
• Superfamily: PHM/PNGase F [ 49742] (2)
• Families:
  • Glycosyl-asparaginase [ 49743]
  • Peptidylglycine alpha-hydroxylating monooxygenase, PHM [ 49746]

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Superfamily statistics

	Genomes (221)	Uniprot 2018_03 genome	PDB chains (SCOP 1.75)
Domains	1,649	8,868	16
Proteins	903	5,190	8

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Functional annotation

• General category: Metabolism
• Detailed category: Redox

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Enzyme Commission (EC)

Highlighted in gray are those with FDR_all>0.001

	EC term	FDR (all)	IC level	SDEO level	Annotation (direct or inherited)
Enzyme Commission (EC)	Peptidylamidoglycolate lyase	0	2.259	--	DIRECT
Enzyme Commission (EC)	With reduced ascorbate as one donor, and incorpora	0	2.259	--	DIRECT
Enzyme Commission (EC)	Peptidylglycine monooxygenase	0.0001696	2.56	--	DIRECT
Enzyme Commission (EC)	Oxidoreductases	0.00000000000004427	0.2975	Least Informative	DIRECT
Enzyme Commission (EC)	Lyases	0.00008747	0.4169	Least Informative	DIRECT
Enzyme Commission (EC)	Acting on paired donors, with incorporation or red	0	1.016	Moderately Informative	DIRECT
Enzyme Commission (EC)	Carbon-nitrogen lyases	0.00000000000005208	1.519	Informative	DIRECT
Enzyme Commission (EC)	Lyases acting on amides, amidines, etc	7.054e-16	1.958	Highly Informative	DIRECT

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Mouse Phenotype (MP)

Highlighted in gray are those with FDR_all>0.001

	MP term	FDR (all)	IC level	SDMP level	Annotation (direct or inherited)
Mammalian Phenotype (MP)	cardiovascular system phenotype	0	0.6818	Least Informative	DIRECT

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Worm Phenotype (WP)

Highlighted in gray are those with FDR_all>0.001

	WP term	FDR (all)	IC level	SDWP level	Annotation (direct or inherited)
Worm Phenotype (WP)	growth variant	0	0.4022	--	DIRECT
Worm Phenotype (WP)	slow growth	0	0.5903	--	DIRECT
Worm Phenotype (WP)	developmental timing variant	0	0.5373	--	DIRECT
Worm Phenotype (WP)	postembryonic development variant	0	0.3347	--	DIRECT
Worm Phenotype (WP)	embryonic lethal	0	0.07108	--	DIRECT
Worm Phenotype (WP)	larval arrest	0	0.5677	--	DIRECT
Worm Phenotype (WP)	lethal	0	0.01121	--	DIRECT
Worm Phenotype (WP)	progeny variant	0	0.7582	--	DIRECT
Worm Phenotype (WP)	fertility variant	0	0.08329	--	DIRECT
Worm Phenotype (WP)	development variant	0	0.001706	--	DIRECT
Worm Phenotype (WP)	morphology variant	0	0.06117	--	DIRECT
Worm Phenotype (WP)	organism development variant	0	0.004279	--	DIRECT
Worm Phenotype (WP)	organism morphology variant	0	0.2011	--	DIRECT
Worm Phenotype (WP)	organ system physiology variant	0	0.05921	--	DIRECT
Worm Phenotype (WP)	organism physiology variant	0	0.1405	--	DIRECT
Worm Phenotype (WP)	organism homeostasis metabolism variant	0	0.1501	--	DIRECT
Worm Phenotype (WP)	reproductive system physiology variant	0	0.07209	--	DIRECT
Worm Phenotype (WP)	maternal sterile	0	0.171	--	DIRECT
Worm Phenotype (WP)	hermaphrodite sterile	0	0.1685	--	DIRECT
Worm Phenotype (WP)	embryonic development variant	0	0.06709	--	DIRECT
Worm Phenotype (WP)	hermaphrodite fertility variant	0	0.1278	--	DIRECT
Worm Phenotype (WP)	developmental growth variant	0	0.5677	--	DIRECT
Worm Phenotype (WP)	hermaphrodite fertility reduced	0	0.1672	--	DIRECT
Worm Phenotype (WP)	fertility reduced	0	0.09267	--	DIRECT
Worm Phenotype (WP)	physiology variant	1	0	--	INHERITED FROM: hermaphrodite fertility variant || developmental growth variant || retarded heterochronic variations || larval lethal || reproductive system physiology variant || organism homeostasis metabolism variant || lethal || larval development variant || sterile progeny || organism physiology variant || progeny variant || slow growth || development variant || developmental timing variant || hermaphrodite sterile || growth variant || hermaphrodite fertility reduced || embryonic development variant || embryonic lethal || larval growth variant || general pace of development variant || fertility variant || postembryonic development variant || larval arrest || organ system physiology variant || maternal sterile || organism development variant || fertility reduced
Worm Phenotype (WP)	sterile	1	0.161	--	INHERITED FROM: hermaphrodite sterile || maternal sterile || sterile progeny
Worm Phenotype (WP)	general pace of development variant	0	0.5708	Least Informative	DIRECT
Worm Phenotype (WP)	larval lethal	0	0.6947	Least Informative	DIRECT
Worm Phenotype (WP)	retarded heterochronic variations	0	0.5373	Least Informative	DIRECT
Worm Phenotype (WP)	larval development variant	0	0.5007	Least Informative	DIRECT
Worm Phenotype (WP)	larval growth variant	0	0.5677	Least Informative	DIRECT
Worm Phenotype (WP)	sterile progeny	0	0.7582	Moderately Informative	DIRECT

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Enzyme Commission (EC)

Highlighted in gray are those with FDR_all>0.001

	EC term	FDR (all)	IC level	SDEC level	Annotation (direct or inherited)
Enzyme Commission (EC)	With reduced ascorbate as one donor, and incorporation of one atom of oxygen	0	2.35	--	DIRECT
Enzyme Commission (EC)	Peptidylamidoglycolate lyase	0	2.475	--	DIRECT
Enzyme Commission (EC)	Peptidylglycine monooxygenase	0.0001749	2.475	--	DIRECT
Enzyme Commission (EC)	Oxidoreductases	0.00000000000002171	0.6234	Least Informative	DIRECT
Enzyme Commission (EC)	Lyases	0.0001721	0.6918	Least Informative	DIRECT
Enzyme Commission (EC)	Acting on paired donors, with incorporation or reduction of molecular oxygen. The oxygen incorporate	0	1.308	Informative	DIRECT
Enzyme Commission (EC)	Carbon-nitrogen lyases	0.00000000005612	1.673	Informative	DIRECT
Enzyme Commission (EC)	Lyases acting on amides, amidines, etc	0.0000000000003759	1.998	Highly Informative	DIRECT

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InterPro annotation

• Cross references: IPR008977 SSF49742 Protein matches
• Abstract:

  Peptidylglycine alpha-hydroxylating monooxygenase (PHM) is a copper-containing enzyme that catalyses an oxygen-dependent hydroxylation of peptide-extended glycine residues. Members of this family bind peptide substrates and consists of two domains of this fold packed together. Structurally, this domain consists of a beta-sandwich of 8 strands in 2 beta-sheets, in a jelly-roll topology [10504734].

InterPro database

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