tRNA-binding arm superfamily

SCOP classification

• Root: SCOP hierarchy in SUPERFAMILY [ 0] (11)
• Class: All alpha proteins [ 46456] (284)
• Fold: Long alpha-hairpin [ 46556] (20)
• Superfamily: tRNA-binding arm [ 46589] (4)
• Families:
  • Seryl-tRNA synthetase (SerRS) [ 46590]
  • Phenylalanyl-tRNA synthetase (PheRS) [ 46593]
  • Valyl-tRNA synthetase (ValRS) C-terminal domain [ 81635]
  • Methicillin resistance protein FemA probable tRNA-binding arm [ 81671]

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Superfamily statistics

	Genomes (3,205)	Uniprot 2018_03 genome	PDB chains (SCOP 1.75)
Domains	9,203	67,585	4
Proteins	9,200	67,565	4

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Functional annotation

• General category: Information
• Detailed category: Translation

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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)	Serine--tRNA ligase	0	2.259	--	DIRECT
Enzyme Commission (EC)	Forming carbon-oxygen bonds	0	1.113	--	DIRECT
Enzyme Commission (EC)	glycyltransferase	0.0000000000003325	2.56	--	DIRECT
Enzyme Commission (EC)	Transferases	1	0	--	INHERITED FROM: glycyltransferase
Enzyme Commission (EC)	Acyltransferases	1	0.8117	--	INHERITED FROM: glycyltransferase
Enzyme Commission (EC)	Ligases	0	0.6568	Least Informative	DIRECT
Enzyme Commission (EC)	Ligases forming aminoacyl-tRNA and related compoun	0	1.113	Moderately Informative	DIRECT
Enzyme Commission (EC)	Phenylalanine--tRNA ligase	0	1.715	Informative	DIRECT
Enzyme Commission (EC)	Aminoacyltransferases	0.2514	1.56	Informative	INHERITED FROM: glycyltransferase
Enzyme Commission (EC)	Valine--tRNA ligase	0	1.958	Highly Informative	DIRECT

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Yeast Phenotype (YP)

Highlighted in gray are those with FDR_all>0.001

	YP term	FDR (all)	IC level	SDYP level	Annotation (direct or inherited)
Yeast Phenotype (YP)	metabolism and growth	0	0.5905	Least Informative	DIRECT
Yeast Phenotype (YP)	vegetative growth	0	1.392	Informative	DIRECT

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Arabidopsis Plant Ontology (AP)

Highlighted in gray are those with FDR_all>0.001

	AP term	FDR (all)	IC level	SDAP level	Annotation (direct or inherited)
Plant ANatomical entity (PAN)	stalk	0	0.7019	--	DIRECT
Plant ANatomical entity (PAN)	plant embryo	0	0.5969	--	DIRECT
Plant ANatomical entity (PAN)	leaf lamina	0	0.7057	--	DIRECT
Plant ANatomical entity (PAN)	gynoecium	0	0.6058	--	DIRECT
Plant ANatomical entity (PAN)	petiole	0	0.7287	--	DIRECT
Plant ANatomical entity (PAN)	inflorescence branch	0	0.6366	--	DIRECT
Plant ANatomical entity (PAN)	phyllome apex	0	0.7019	--	DIRECT
Plant ANatomical entity (PAN)	stamen	0	0.6028	--	DIRECT
Plant ANatomical entity (PAN)	epidermal cell	0	0.2569	--	DIRECT
Plant ANatomical entity (PAN)	shoot epidermis	0	0.2691	--	DIRECT
Plant ANatomical entity (PAN)	stem	0	0.577	--	DIRECT
Plant ANatomical entity (PAN)	cardinal organ part	0	0.51	--	DIRECT
Plant ANatomical entity (PAN)	perianth	0	0.5448	--	DIRECT
Plant ANatomical entity (PAN)	phyllome	0	0.3809	--	DIRECT
Plant ANatomical entity (PAN)	corolla	0	0.594	--	DIRECT
Plant ANatomical entity (PAN)	sporophyll	0	0.4713	--	DIRECT
Plant ANatomical entity (PAN)	lamina	0	0.7057	--	DIRECT
Plant ANatomical entity (PAN)	cauline leaf	0	0.7019	--	DIRECT
Plant ANatomical entity (PAN)	shoot system	0	0.05747	--	DIRECT
Plant ANatomical entity (PAN)	shoot epidermal cell	0	0.276	--	DIRECT
Plant ANatomical entity (PAN)	androecium	0	0.594	--	DIRECT
Plant ANatomical entity (PAN)	reproductive shoot system	0	0.4141	--	DIRECT
Plant ANatomical entity (PAN)	plant cell	0	0.1489	--	DIRECT
Plant ANatomical entity (PAN)	epidermis	0	0.2464	--	DIRECT
Plant ANatomical entity (PAN)	pedicel	0	0.6366	--	DIRECT
Plant ANatomical entity (PAN)	collective plant structure	0	0.01577	--	DIRECT
Plant ANatomical entity (PAN)	portion of plant tissue	0	0.1892	--	DIRECT
Plant ANatomical entity (PAN)	inflorescence axis	0	0.6366	--	DIRECT
Plant ANatomical entity (PAN)	leaf lamina base	0	0.7094	--	DIRECT
Plant ANatomical entity (PAN)	petal	0	0.594	--	DIRECT
Plant ANatomical entity (PAN)	calyx	0	0.5715	--	DIRECT
Plant ANatomical entity (PAN)	plant organ	0	0.2816	--	DIRECT
Plant ANatomical entity (PAN)	carpel	0	0.6087	--	DIRECT
Plant ANatomical entity (PAN)	leaf apex	0	0.7094	--	DIRECT
Plant ANatomical entity (PAN)	plant axis	0	0.3881	--	DIRECT
Plant ANatomical entity (PAN)	multi-tissue plant structure	0	0.2691	--	DIRECT
Plant ANatomical entity (PAN)	sepal	0	0.5715	--	DIRECT
Plant ANatomical entity (PAN)	stomatal complex	0	0.2774	--	DIRECT
Plant ANatomical entity (PAN)	collective leaf structure	0	0.55	--	DIRECT
Plant ANatomical entity (PAN)	shoot apex	0	0.5633	--	DIRECT
Plant ANatomical entity (PAN)	vascular leaf	0	0.5246	--	DIRECT
Plant ANatomical entity (PAN)	branch	0	0.6366	--	DIRECT
Plant ANatomical entity (PAN)	organ lamina	1	0.7057	--	INHERITED FROM: leaf lamina base || leaf lamina
Plant ANatomical entity (PAN)	collective plant organ structure	1	0.04502	--	INHERITED FROM: inflorescence axis || calyx || flower || sporophyll || inflorescence meristem || inflorescence || perianth || stem || leaf || phyllome || sepal || vascular leaf || gynoecium || petiole || petal || reproductive shoot system || shoot apex || leaf apex || carpel || collective phyllome structure || guard cell || megasporophyll || cauline leaf || microsporophyll || leaf lamina || shoot epidermal cell || corolla || pedicel || androecium || stomatal complex || phyllome apex || cotyledon || stamen || inflorescence branch || shoot axis || shoot system || leaf lamina base || collective leaf structure || branch || shoot epidermis
Plant ANatomical entity (PAN)	plant structure	1	0	--	INHERITED FROM: perianth || sporophyll || calyx || inflorescence axis || flower || lamina || collective plant structure || plant embryo || leaf || phyllome || cardinal organ part || multi-tissue plant structure || microsporophyll || guard cell || megasporophyll || cauline leaf || reproductive shoot system || shoot apex || leaf apex || leaf lamina base || branch || collective leaf structure || inflorescence branch || shoot system || portion of plant tissue || stomatal complex || plant organ || portion of meristem tissue || stem || whole plant || inflorescence meristem || epidermis || inflorescence || cardinal part of multi-tissue plant structure || petiole || stalk || gynoecium || vascular leaf || sepal || epidermal cell || leaf lamina || shoot epidermal cell || corolla || plant axis || collective phyllome structure || petal || plant cell || carpel || seed || shoot epidermis || phyllome apex || cotyledon || stamen || shoot axis || pedicel || androecium
Plant ANatomical entity (PAN)	phyllome lamina	1	0.7057	--	INHERITED FROM: leaf lamina base || leaf lamina
Plant ANatomical entity (PAN)	leaf	0	0.5053	Least Informative	DIRECT
Plant ANatomical entity (PAN)	megasporophyll	0	0.6087	Least Informative	DIRECT
Plant ANatomical entity (PAN)	collective phyllome structure	0	0.4648	Least Informative	DIRECT
Plant ANatomical entity (PAN)	seed	0	0.6087	Least Informative	DIRECT
Plant ANatomical entity (PAN)	guard cell	0	0.2774	Least Informative	DIRECT
Plant ANatomical entity (PAN)	portion of meristem tissue	0	0.6838	Least Informative	DIRECT
Plant ANatomical entity (PAN)	whole plant	0	0.4218	Least Informative	DIRECT
Plant ANatomical entity (PAN)	shoot axis	0	0.4735	Least Informative	DIRECT
Plant ANatomical entity (PAN)	cardinal part of multi-tissue plant structure	0	0.5029	Least Informative	DIRECT
Plant ANatomical entity (PAN)	flower	0	0.4337	Least Informative	DIRECT
Plant ANatomical entity (PAN)	microsporophyll	0	0.5029	Least Informative	DIRECT
Plant ANatomical entity (PAN)	inflorescence	0	0.5969	Least Informative	DIRECT
Plant ANatomical entity (PAN)	cotyledon	0	0.7615	Moderately Informative	DIRECT
Plant ANatomical entity (PAN)	inflorescence meristem	0	0.7789	Moderately Informative	DIRECT
Plant structure DEvelopment stage (PDE)	leaf production stage	0	0.3937	--	DIRECT
Plant structure DEvelopment stage (PDE)	1 main shoot growth stage	0	0.3937	--	DIRECT
Plant structure DEvelopment stage (PDE)	whole plant development stage	0	0.1968	--	DIRECT
Plant structure DEvelopment stage (PDE)	plant organ development stage	0	0.08108	--	DIRECT
Plant structure DEvelopment stage (PDE)	plant embryo stage	0	0.2833	--	DIRECT
Plant structure DEvelopment stage (PDE)	floral organ formation stage	0	0.0937	--	DIRECT
Plant structure DEvelopment stage (PDE)	collective plant organ structure development stage	0	0.03771	--	DIRECT
Plant structure DEvelopment stage (PDE)	floral organ differentiation stage	0	0.0937	--	DIRECT
Plant structure DEvelopment stage (PDE)	corolla development stage	0	0.1981	--	DIRECT
Plant structure DEvelopment stage (PDE)	flowering stage	0	0.2162	--	DIRECT
Plant structure DEvelopment stage (PDE)	sporophyte vegetative stage	0	0.2036	--	DIRECT
Plant structure DEvelopment stage (PDE)	collective phyllome structure development stage	0	0.0937	--	DIRECT
Plant structure DEvelopment stage (PDE)	phyllome development stage	0	0.4754	--	DIRECT
Plant structure DEvelopment stage (PDE)	reproductive shoot system development stage	0	0.05008	--	DIRECT
Plant structure DEvelopment stage (PDE)	life of whole plant stage	1	0.2022	--	INHERITED FROM: sporophyte vegetative stage || C globular stage || LP.10 ten leaves visible stage || E expanded cotyledon stage || LP.12 twelve leaves visible stage || F mature embryo stage || LP.04 four leaves visible stage || D bilateral stage || LP.06 six leaves visible stage || LP.08 eight leaves visible stage || LP.02 two leaves visible stage || plant embryo stage || leaf production stage || 1 main shoot growth stage
Plant structure DEvelopment stage (PDE)	flower development stage	1	0.07083	--	INHERITED FROM: corolla development stage || flowering stage || floral organ differentiation stage || floral organ formation stage
Plant structure DEvelopment stage (PDE)	leaf development stage	1	0.4754	--	INHERITED FROM: 4 leaf senescence stage
Plant structure DEvelopment stage (PDE)	shoot system development stage	1	0.04053	--	INHERITED FROM: phyllome development stage || reproductive shoot system development stage || floral organ formation stage || floral organ differentiation stage || flowering stage || corolla development stage || plant organ development stage || 4 leaf senescence stage
Plant structure DEvelopment stage (PDE)	sporophyte development stage	1	0.2022	--	INHERITED FROM: LP.08 eight leaves visible stage || LP.12 twelve leaves visible stage || E expanded cotyledon stage || LP.10 ten leaves visible stage || LP.06 six leaves visible stage || sporophyte vegetative stage || C globular stage || leaf production stage || 1 main shoot growth stage || D bilateral stage || F mature embryo stage || LP.04 four leaves visible stage || plant embryo stage || LP.02 two leaves visible stage
Plant structure DEvelopment stage (PDE)	4 leaf senescence stage	0	0.478	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	D bilateral stage	0	0.3729	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.02 two leaves visible stage	0	0.5603	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	F mature embryo stage	0	0.4088	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.04 four leaves visible stage	0	0.4338	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	E expanded cotyledon stage	0	0.353	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.10 ten leaves visible stage	0	0.513	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.08 eight leaves visible stage	0	0.586	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.12 twelve leaves visible stage	0	0.5666	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	C globular stage	0	0.3937	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.06 six leaves visible stage	0	0.5243	Least 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)	Ligases forming aminoacyl-tRNA and related compounds	0	1.52	--	DIRECT
Enzyme Commission (EC)	Serine--tRNA ligase	0	2.651	--	DIRECT
Enzyme Commission (EC)	Valine--tRNA ligase	0	2.253	--	DIRECT
Enzyme Commission (EC)	glycyltransferase	0.0000000000001765	2.651	--	DIRECT
Enzyme Commission (EC)	Transferases	1	0.3035	--	INHERITED FROM: glycyltransferase
Enzyme Commission (EC)	Acyltransferases	1	0.8446	--	INHERITED FROM: glycyltransferase
Enzyme Commission (EC)	Ligases	0	0.9606	Moderately Informative	DIRECT
Enzyme Commission (EC)	Aminoacyltransferases	1	1.166	Moderately Informative	INHERITED FROM: glycyltransferase
Enzyme Commission (EC)	Forming carbon-oxygen bonds	0	1.505	Informative	DIRECT
Enzyme Commission (EC)	Phenylalanine--tRNA ligase	0	2.107	Highly Informative	DIRECT

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InterPro annotation

• Cross references: IPR010978 SSF46589 Protein matches
• Abstract:

  This entry represents an alpha-helical tRNA-binding arm found in class I and II aminoacyl-tRNA synthetase enzymes, as well as in the methicillin resistance protein FemA.

  The tRNA-binding arm domain is conserved between class I and class II aminoacyl-tRNA synthetase enzymes , consisting of two alpha helices in an antiparallel hairpin with a left-handed twist. The appended tRNA-binding domains recognize a small number of nucleotides that are conserved specifically in each cognate tRNA species for the discrimination between the cognate and noncognate tRNAs [12554880]. These nucleotides are called identity elements, and constitute the identity set. The tRNA-binding arm occurs as the C-terminal domain in some class I enzymes, such as valyl-tRNA synthetase, and as the N-terminal domain in some class II enzymes, such as phenylalanyl-tRNA synthetase.

  The methicillin resistance protein, FemA (factors essential for methicillin resistance), contains a probable tRNA-binding arm that is similar in structure to those found in tRNA synthetases. In FemA, the tRNA-binding arm is inserted into the C-terminal NAT-like domain, and is thought to bind tRNA-glycine. FemA, along with FemB and FemX, plays a vital role in peptidoglycan biosynthesis specific to Staphylococci [12176388].

InterPro database

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