Alanine racemase C-terminal domain-like superfamily

SCOP classification

• Root: SCOP hierarchy in SUPERFAMILY [ 0] (11)
• Class: All beta proteins [ 48724] (174)
• Fold: Domain of alpha and beta subunits of F1 ATP synthase-like [ 50614] (3)
• Superfamily: Alanine racemase C-terminal domain-like [ 50621] (2)
• Families:
  • Alanine racemase [ 88682]
  • Eukaryotic ODC-like [ 88683] (2)

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Superfamily statistics

	Genomes (2,947)	Uniprot 2018_03 genome	PDB chains (SCOP 1.75)
Domains	8,929	70,727	18
Proteins	8,887	70,615	15

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Functional annotation

• General category: Metabolism
• Detailed category: Amino acids metabolism and transport

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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)	Diaminopimelate decarboxylase	0	2.259	--	DIRECT
Enzyme Commission (EC)	Ornithine decarboxylase	0	2.259	--	DIRECT
Enzyme Commission (EC)	Carbon-carbon lyases	0	0.8275	--	DIRECT
Enzyme Commission (EC)	Alanine racemase	0	2.259	--	DIRECT
Enzyme Commission (EC)	Lyases	0	0.4169	Least Informative	DIRECT
Enzyme Commission (EC)	Isomerases	0	0.5914	Least Informative	DIRECT
Enzyme Commission (EC)	Racemases and epimerases	0	1.238	Moderately Informative	DIRECT
Enzyme Commission (EC)	Carboxy-lyases	0	0.9578	Moderately Informative	DIRECT
Enzyme Commission (EC)	Acting on amino acids and derivatives	0	1.657	Informative	DIRECT
Enzyme Commission (EC)	Arginine decarboxylase	0	2.083	Highly Informative	DIRECT

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Disease Ontology (DO)

Highlighted in gray are those with FDR_all>0.001

	DO term	FDR (all)	IC level	SDDO level	Annotation (direct or inherited)
Disease Ontology (DO)	disease of cellular proliferation	0	0.2812	--	DIRECT
Disease Ontology (DO)	cancer	0	0.3104	--	DIRECT

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Xenopus Anatomy (XA)

Highlighted in gray are those with FDR_all>0.001

	XA term	FDR (all)	IC level	SDXA level	Annotation (direct or inherited)
Xenopus ANatomical entity (XAN)	egg	0	1.17	--	DIRECT
Xenopus ANatomical entity (XAN)	gonad	0	0.8318	--	DIRECT
Xenopus ANatomical entity (XAN)	genital system	0	0.5909	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical group	0	0.1442	--	DIRECT
Xenopus ANatomical entity (XAN)	head region	0	0.5108	--	DIRECT
Xenopus ANatomical entity (XAN)	gamete	0	1.17	--	DIRECT
Xenopus ANatomical entity (XAN)	organism subdivision	0	0.1871	--	DIRECT
Xenopus ANatomical entity (XAN)	tail region	0	1.284	--	DIRECT
Xenopus ANatomical entity (XAN)	compound organ	0	0.24	--	DIRECT
Xenopus ANatomical entity (XAN)	cell	0	0.7974	--	DIRECT
Xenopus ANatomical entity (XAN)	primary germ layer	0	0.7237	--	DIRECT
Xenopus ANatomical entity (XAN)	trunk region	0	0.4287	--	DIRECT
Xenopus ANatomical entity (XAN)	male genitalia	0	0.8318	--	DIRECT
Xenopus ANatomical entity (XAN)	otic vesicle	0	1.647	--	DIRECT
Xenopus ANatomical entity (XAN)	multicellular anatomical structure	0	0.1217	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical region	0	0.193	--	DIRECT
Xenopus ANatomical entity (XAN)	central nervous system	0	0.6506	--	DIRECT
Xenopus ANatomical entity (XAN)	male organism	0	0.8318	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical structure	0	0	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical cluster	0	0.7974	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical system	1	0.3094	--	INHERITED FROM: testis || alimentary system || urogenital system || intestine || nervous system || forebrain || brain || egg || genital system || vestibuloauditory system || sensory system || male genitalia || central nervous system || otic vesicle || gamete
Xenopus ANatomical entity (XAN)	whole organism	1	0.09747	--	INHERITED FROM: urogenital system || tail region || head region || genital system || brain || egg || intestine || forebrain || nervous system || alimentary system || anatomical group || testis || cavitated compound organ || multicellular anatomical structure || gonad || ectoderm || compound organ || tail || trunk || tissue || anatomical region || germ cell || otic vesicle || limb || central nervous system || male genitalia || pharyngeal region || gamete || trunk region || anatomical cluster || viscus || male organism || endomesoderm || sensory system || multi-tissue structure || vestibuloauditory system || organism subdivision || embryonic structure || cell || head || primary germ layer
Xenopus ANatomical entity (XAN)	nervous system	0	0.6341	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	trunk	0	0.4308	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	cavitated compound organ	0	0.3033	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	embryo	0	0.6341	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	urogenital system	0	0.5011	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	tissue	0	0.5011	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	head	0	0.5108	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	sensory system	0	1.17	Moderately Informative	DIRECT
Xenopus ANatomical entity (XAN)	multi-tissue structure	0	1.071	Moderately Informative	DIRECT
Xenopus ANatomical entity (XAN)	germ cell	0	1.013	Moderately Informative	DIRECT
Xenopus ANatomical entity (XAN)	viscus	0	0.9618	Moderately Informative	DIRECT
Xenopus ANatomical entity (XAN)	ectoderm	0	0.9688	Moderately Informative	DIRECT
Xenopus ANatomical entity (XAN)	alimentary system	0	0.955	Moderately Informative	DIRECT
Xenopus ANatomical entity (XAN)	embryonic structure	0	1.138	Moderately Informative	DIRECT
Xenopus ANatomical entity (XAN)	testis	0	0.8318	Moderately Informative	DIRECT
Xenopus ANatomical entity (XAN)	brain	0	0.8635	Moderately Informative	DIRECT
Xenopus ANatomical entity (XAN)	endomesoderm	0	1.256	Informative	DIRECT
Xenopus ANatomical entity (XAN)	pharyngeal region	0	1.482	Informative	DIRECT
Xenopus ANatomical entity (XAN)	forebrain	0	1.682	Informative	DIRECT
Xenopus ANatomical entity (XAN)	tail	0	1.399	Informative	DIRECT
Xenopus ANatomical entity (XAN)	anatomical entity in vitro	0	1.314	Informative	DIRECT
Xenopus ANatomical entity (XAN)	intestine	0	1.363	Informative	DIRECT
Xenopus ANatomical entity (XAN)	limb	0	1.615	Informative	DIRECT
Xenopus ANatomical entity (XAN)	vestibuloauditory system	0	1.531	Informative	DIRECT
Xenopus DEvelopment stage (XDE)	metamorphosing tadpole stage	0	0.6715	--	DIRECT
Xenopus DEvelopment stage (XDE)	tadpole stage	0	0.5946	--	DIRECT
Xenopus DEvelopment stage (XDE)	NF stage	0	0.02327	--	DIRECT
Xenopus DEvelopment stage (XDE)	post-embryonic stage	0	0.5693	Least Informative	DIRECT
Xenopus DEvelopment stage (XDE)	unspecified stage	0	1.131	Moderately Informative	DIRECT
Xenopus DEvelopment stage (XDE)	climax stage	0	0.7597	Moderately Informative	DIRECT
Xenopus DEvelopment stage (XDE)	NF stage 66	0	1.384	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)	Ornithine decarboxylase	0	2.35	--	DIRECT
Enzyme Commission (EC)	Arginine decarboxylase	0	2.35	--	DIRECT
Enzyme Commission (EC)	Diaminopimelate decarboxylase	0	2.651	--	DIRECT
Enzyme Commission (EC)	Alanine racemase	0	2.651	--	DIRECT
Enzyme Commission (EC)	Carboxynorspermidine decarboxylase	0.00000004603	2.651	--	DIRECT
Enzyme Commission (EC)	Lyases	0	0.6918	Least Informative	DIRECT
Enzyme Commission (EC)	Carbon-carbon lyases	0	1.101	Moderately Informative	DIRECT
Enzyme Commission (EC)	Isomerases	0	0.8446	Moderately Informative	DIRECT
Enzyme Commission (EC)	Carboxy-lyases	0	1.253	Informative	DIRECT
Enzyme Commission (EC)	Racemases and epimerases	0	1.447	Informative	DIRECT
Enzyme Commission (EC)	Acting on amino acids and derivatives	0	1.952	Highly Informative	DIRECT

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InterPro annotation

• Cross references: IPR009006 SSF50621 Protein matches
• Abstract:

  This entry represents a beta-barrel domain found at the C-terminal of alanine racemase and in group IV pyridoxal-5'-phosphate (PLP)-dependent decarboxylases, such as eukaryotic ornithine decarboxylase , arginine decarboxylase and diaminopimelate decarboxylase . These enzymes belong to the same structural family.

  Alanine racemase plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine. Proteins contains this domain are found in both prokaryotic and eukaryotic proteins [1676385,7871888]. The molecular structure of alanine racemase from Bacillus stearothermophilus was determined by X-ray crystallography to a resolution of 1.9 A [9063881]. The alanine racemase monomer is composed of two domains, an eight-stranded alpha/beta barrel at the N-terminus, and a C-terminal domain essentially composed of beta-strand. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above the mouth of the alpha/beta barrel and is covalently linked via an aldimine linkage to a lysine residue, which is at the C-terminus of the first beta-strand of the alpha/beta barrel.

  Eukaryotic ornithine decarboxylase (ODC) acts as a homodimer to produce putrescine (1,4-diaminobutane) from ornithine, where putrescine is the precursor of other polyamines in animals, plants, and bacteria. Arginine decarboxylase is also involved in putrescine biosynthesis. This is the first committed step in polyamine biosynthesis. Alanine racemase is a structurally homologous enzyme. Both proteins share a common alpha/beta barrel that binds the cofactor via a Schiff base on the C-terminal end of the barrel [10378276].

  Diaminopimelate decarboxylase (DapDC) catalyzes the final step of lysine biosynthesis in bacteria.

InterPro database

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