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Trimeric LpxA-like enzymes superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Single-stranded left-handed beta-helix [ 51160] (4)
Superfamily:   Trimeric LpxA-like enzymes [ 51161] (8)
Families:   UDP N-acetylglucosamine acyltransferase [ 51162]
  Tetrahydrodipicolinate-N-succinlytransferase, THDP-succinlytransferase, DapD [ 51165]
  Galactoside acetyltransferase-like [ 51168] (3)
  GlmU C-terminal domain-like [ 51171] (3)
  gamma-carbonic anhydrase-like [ 51174] (3)
  Serine acetyltransferase [ 110309]
  YdcK-like [ 141583]
  PglD-like [ 159280]


Superfamily statistics
Genomes (3,157) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 27,141 153,614 29
Proteins 26,138 150,595 29


Functional annotation
General category Metabolism
Detailed category Other enzymes

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular macromolecule metabolic process0.84170.9642Least InformativeInherited
Biological Process (BP)biosynthetic process0.075770.0000000527Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.38031Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)single-organism metabolic process10.4451Least InformativeInherited
Biological Process (BP)organelle organization0.20191Moderately InformativeInherited
Biological Process (BP)macromolecular complex subunit organization0.00012830.0445Moderately InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.13420.009303Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.0017980.000000000765Moderately InformativeInherited
Biological Process (BP)polysaccharide metabolic process0.00043670.0000000000002018InformativeDirect
Biological Process (BP)microtubule-based process0.0000000046150.00003InformativeDirect
Biological Process (BP)carbohydrate biosynthetic process0.00011010.00000001034InformativeDirect
Biological Process (BP)cellular carbohydrate metabolic process0.00390.00000005604InformativeInherited
Biological Process (BP)cellular metabolic compound salvage0.0032170.0000151InformativeInherited
Biological Process (BP)cell cycle process0.0032370.274InformativeInherited
Biological Process (BP)mitotic cell cycle0.00020450.0371InformativeInherited
Biological Process (BP)cytoskeleton organization0.0040880.2792InformativeInherited
Biological Process (BP)spindle organization0.000025830.00004944Highly InformativeDirect
Biological Process (BP)photorespiration0.000011110.000000000004862Highly InformativeDirect
Biological Process (BP)serine family amino acid metabolic process0.0027230.002336Highly InformativeInherited
Molecular Function (MF)transferase activity0.000081560.0000000000005244Least InformativeDirect
Molecular Function (MF)lyase activity0.011230.123Moderately InformativeInherited
Molecular Function (MF)transferase activity, transferring acyl groups0.00000000000035510InformativeDirect
Molecular Function (MF)hydro-lyase activity0.0000060220.00003088InformativeDirect
Molecular Function (MF)O-acyltransferase activity0.011420.004464Highly InformativeInherited
Molecular Function (MF)acetyltransferase activity0.083290.1906Highly InformativeInherited
Cellular Component (CC)protein complex0.000088490.0008108Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.0021870.7251Least InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle0.000084580.3303Least InformativeInherited
Cellular Component (CC)cytoskeleton0.0000000025480.0002437Moderately InformativeDirect
Cellular Component (CC)actin cytoskeleton0.000091250.00005055InformativeDirect
Cellular Component (CC)microtubule cytoskeleton0.00000000000058470.0000002104InformativeDirect
Cellular Component (CC)microtubule associated complex0.0000000000026050.0000000001241Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) biosynthetic process 0.0000000527 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.4451 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.9642 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.000000000765 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00002542 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 0.07571 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.437 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.1619 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.05352 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.8736 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.634 Moderately Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 0.185 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.00101 Moderately Informative Inherited
Biological Process (BP) system process 0.695 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.8613 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.1754 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.07073 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.0445 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.009303 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.4015 Moderately Informative Inherited
Biological Process (BP) gene expression 0.3229 Moderately Informative Inherited
Biological Process (BP) polysaccharide metabolic process 0.0000000000002018 Informative Direct
Biological Process (BP) microtubule-based process 0.00003 Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 0.0004165 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.00000001034 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 0.0000151 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0.00000005604 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0007091 Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 0.004291 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.00553 Informative Inherited
Biological Process (BP) regulation of purine nucleotide metabolic process 0.001343 Informative Inherited
Biological Process (BP) sulfur amino acid metabolic process 0.0101 Informative Inherited
Biological Process (BP) sulfur compound biosynthetic process 0.04671 Informative Inherited
Biological Process (BP) central nervous system development 0.151 Informative Inherited
Biological Process (BP) cell cycle process 0.274 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.0371 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.2792 Informative Inherited
Biological Process (BP) cellular component movement 0.4942 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.004849 Informative Inherited
Biological Process (BP) translational initiation 0.00000008287 Highly Informative Direct
Biological Process (BP) regulation of translation 0.0001278 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0.0003966 Highly Informative Direct
Biological Process (BP) spindle organization 0.00004944 Highly Informative Direct
Biological Process (BP) response to heat 0.000501 Highly Informative Direct
Biological Process (BP) response to carbohydrate stimulus 0.0002515 Highly Informative Direct
Biological Process (BP) photorespiration 0.000000000004862 Highly Informative Direct
Biological Process (BP) glial cell differentiation 0.0000536 Highly Informative Direct
Biological Process (BP) cellular polysaccharide biosynthetic process 0.000000003403 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 0.0002113 Highly Informative Direct
Biological Process (BP) response to drug 0.003296 Highly Informative Inherited
Biological Process (BP) serine family amino acid metabolic process 0.002336 Highly Informative Inherited
Biological Process (BP) regulation of membrane potential 0.001387 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.0000000000005244 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0.009057 Moderately Informative Inherited
Molecular Function (MF) lyase activity 0.123 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.4341 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 7.995e-16 Informative Direct
Molecular Function (MF) hydro-lyase activity 0.00003088 Informative Direct
Molecular Function (MF) GTPase regulator activity 0.00004693 Informative Direct
Molecular Function (MF) RNA binding 0.001623 Informative Inherited
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0.0000003921 Highly Informative Direct
Molecular Function (MF) translation factor activity, nucleic acid binding 0.00000008731 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 0.1906 Highly Informative Inherited
Molecular Function (MF) O-acyltransferase activity 0.004464 Highly Informative Inherited
Molecular Function (MF) adenylyltransferase activity 0.02891 Highly Informative Inherited
Cellular Component (CC) protein complex 0.0008108 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.7251 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.3303 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.4353 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0.0002437 Moderately Informative Direct
Cellular Component (CC) actin cytoskeleton 0.00005055 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.0000002104 Informative Direct
Cellular Component (CC) microtubule associated complex 0.0000000001241 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0.01476Least InformativeInherited
Plant ANatomical entity (PAN)root system0.04008Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.1159Least InformativeInherited
Plant ANatomical entity (PAN)leaf0.2297Least InformativeInherited
Plant ANatomical entity (PAN)vascular system0.0000000001829InformativeDirect
Plant ANatomical entity (PAN)portion of ground tissue0.000006024InformativeDirect
Plant ANatomical entity (PAN)fruit0.00003454InformativeDirect
Plant ANatomical entity (PAN)parenchyma cell0.00000000001298Highly InformativeDirect
Plant ANatomical entity (PAN)phloem0.0000000034Highly InformativeDirect
Plant ANatomical entity (PAN)root stele0.00004112Highly InformativeDirect
Plant ANatomical entity (PAN)mesophyll1Highly InformativeInherited

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Acyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0Moderately InformativeDirect
Biological processCarbohydrate metabolism0Moderately InformativeDirect
Biological processLipid metabolism0Moderately InformativeDirect
Biological processCell shape0InformativeDirect
Biological processLipid biosynthesis0InformativeDirect
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processDiaminopimelate biosynthesis0Highly InformativeDirect
Biological processGlycogen biosynthesis0Highly InformativeDirect
Biological processLipid A biosynthesis0Highly InformativeDirect
Biological processLysine biosynthesis0Highly InformativeDirect
Biological processPeptidoglycan synthesis0Highly InformativeDirect
Biological processCysteine biosynthesis0.000000299Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPlastid1Moderately InformativeInherited
Cellular componentKinetochore0.0000002521Highly InformativeDirect
Cellular componentCentromere0.00002083Highly InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationAcyltransferase0InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0Least InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)amine and polyamine metabolism0.0004451Moderately InformativeDirect
UniPathway (UP)L-lysine biosynthesis via DAP pathway0InformativeDirect
UniPathway (UP)carnitine metabolism0InformativeDirect
UniPathway (UP)L-cysteine metabolism0.0000008058InformativeDirect
UniPathway (UP)L-cysteine biosynthesis0.000002102Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR011004 SSF51161 Protein matches
Abstract

This domain is characterised by trimeric LpxA-like enzymes that display a single-stranded left-handed beta-helix fold, composed of tandem repeats of a hexapeptide, as represented by the Bacterial transferase hexapeptide repeat, where the hexapeptide repeats correspond to individual strands. Many bacterial transferases contain this domain. The structures of several proteins with this domain have been determined, including UDP N-acetylglucosamine acyltransferase (LpxA, ) from Escherichia coli, the first enzyme in the lipid A biosynthetic pathway [PubMed7481807]; galactoside acetyltransferase (GAT, LacA, ) from E. coli, a gene product of the lac operon that may assist cellular detoxification [PubMed11937062]; gamma-class Archaeon carbonic anhydrase , a zinc-containing enzyme that catalyses the reversible hydration of carbon dioxide [PubMed10924115]; tetrahydrodipicolinate-N-succinlytransferase (DapD) from Mycobacterium bovis, an enzyme from the lysine biosynthetic pathway that contains an extra N-terminal 3-helical domain [PubMed11910040]; and the C-terminal domain of N-acetylglucosamine 1-phosphate uridyltransferase (GlmU, ) from E. coli, a trimeric bifunctional enzyme that catalyses the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine, an essential precursor for many biomolecules [PubMed11329257].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 18 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Trimeric LpxA-like enzymes domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 18 hidden Markov models representing the Trimeric LpxA-like enzymes superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]