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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 component organization or biogenesis0.27171Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.85430.9645Least InformativeInherited
Biological Process (BP)biosynthetic process0.08240.000000207Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)single-organism metabolic process10.5342Least InformativeInherited
Biological Process (BP)cellular component biogenesis0.27690.2859Moderately InformativeInherited
Biological Process (BP)macromolecular complex subunit organization0.00002780.009117Moderately InformativeInherited
Biological Process (BP)organelle organization0.21031Moderately InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.13640.008824Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.0019490.0000000007721Moderately InformativeInherited
Biological Process (BP)polysaccharide metabolic process0.0004670.0000000000002493InformativeDirect
Biological Process (BP)microtubule-based process0.0000000052580.00003319InformativeDirect
Biological Process (BP)carbohydrate biosynthetic process0.00010890.00000001021InformativeDirect
Biological Process (BP)protein oligomerization0.023080.009191InformativeInherited
Biological Process (BP)cellular carbohydrate metabolic process0.0041130.00000005591InformativeInherited
Biological Process (BP)cellular metabolic compound salvage0.0031930.00001479InformativeInherited
Biological Process (BP)cell cycle process0.0033810.284InformativeInherited
Biological Process (BP)mitotic cell cycle0.00021620.03875InformativeInherited
Biological Process (BP)cytoskeleton organization0.0042670.2889InformativeInherited
Biological Process (BP)spindle organization0.000056470.0001368Highly InformativeDirect
Biological Process (BP)photorespiration0.000011580.000000000005304Highly InformativeDirect
Biological Process (BP)protein homooligomerization0.00026430.0002303Highly InformativeDirect
Biological Process (BP)serine family amino acid metabolic process0.0027270.002352Highly InformativeInherited
Molecular Function (MF)transferase activity0.000036270.00000000000008864Least InformativeDirect
Molecular Function (MF)lyase activity0.013480.1388Moderately InformativeInherited
Molecular Function (MF)transferase activity, transferring acyl groups0.000000000000051560InformativeDirect
Molecular Function (MF)hydro-lyase activity0.0000063690.00003381InformativeDirect
Molecular Function (MF)O-acyltransferase activity0.0043570.000913Highly InformativeInherited
Molecular Function (MF)acetyltransferase activity0.059780.1201Highly InformativeInherited
Cellular Component (CC)protein complex0.00010280.0009626Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.0025230.7549Least InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle0.00009550.3502Least InformativeInherited
Cellular Component (CC)cytoskeleton0.000000002920.0002846Moderately InformativeDirect
Cellular Component (CC)actin cytoskeleton0.000094720.00004894InformativeDirect
Cellular Component (CC)microtubule cytoskeleton0.00000000000065690.0000002426InformativeDirect
Cellular Component (CC)microtubule associated complex0.0000000000023330.0000000001144Highly 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 0.000000207 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.5342 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 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 0.9645 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) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.0000000007721 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00002514 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 0.07585 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.4409 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.2859 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.009117 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.1688 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.05373 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 0.8955 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.659 Moderately Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 0.1965 Moderately Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.001013 Moderately Informative Inherited
Biological Process (BP) system process 0.7141 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 0.8829 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.1915 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.07728 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.008824 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 0.423 Moderately Informative Inherited
Biological Process (BP) gene expression 0.323 Moderately Informative Inherited
Biological Process (BP) polysaccharide metabolic process 0.0000000000002493 Informative Direct
Biological Process (BP) microtubule-based process 0.00003319 Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 0.0003552 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.00000001021 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 0.00001479 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0.00000005591 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0007035 Informative Direct
Biological Process (BP) protein oligomerization 0.009191 Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 0.003557 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.005817 Informative Inherited
Biological Process (BP) regulation of purine nucleotide metabolic process 0.001241 Informative Inherited
Biological Process (BP) sulfur amino acid metabolic process 0.01015 Informative Inherited
Biological Process (BP) sulfur compound biosynthetic process 0.04719 Informative Inherited
Biological Process (BP) central nervous system development 0.1592 Informative Inherited
Biological Process (BP) cell cycle process 0.284 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.03875 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.2889 Informative Inherited
Biological Process (BP) cellular component movement 0.5062 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.005208 Informative Inherited
Biological Process (BP) translational initiation 0.00000008315 Highly Informative Direct
Biological Process (BP) regulation of translation 0.0001346 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0.0003963 Highly Informative Direct
Biological Process (BP) spindle organization 0.0001368 Highly Informative Direct
Biological Process (BP) response to heat 0.0005295 Highly Informative Direct
Biological Process (BP) response to carbohydrate stimulus 0.0002759 Highly Informative Direct
Biological Process (BP) photorespiration 0.000000000005304 Highly Informative Direct
Biological Process (BP) glial cell differentiation 0.00005679 Highly Informative Direct
Biological Process (BP) cellular polysaccharide biosynthetic process 0.000000003287 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 0.00027 Highly Informative Direct
Biological Process (BP) positive regulation of GTPase activity 0.00006227 Highly Informative Direct
Biological Process (BP) protein homooligomerization 0.0002303 Highly Informative Direct
Biological Process (BP) response to drug 0.003663 Highly Informative Inherited
Biological Process (BP) serine family amino acid metabolic process 0.002352 Highly Informative Inherited
Biological Process (BP) regulation of membrane potential 0.001521 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.00000000000008864 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0.009792 Moderately Informative Inherited
Molecular Function (MF) lyase activity 0.1388 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.4535 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 8.006e-16 Informative Direct
Molecular Function (MF) hydro-lyase activity 0.00003381 Informative Direct
Molecular Function (MF) GTPase regulator activity 0.0000512 Informative Direct
Molecular Function (MF) RNA binding 0.001718 Informative Inherited
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0.0000004303 Highly Informative Direct
Molecular Function (MF) translation factor activity, nucleic acid binding 0.00000008977 Highly Informative Direct
Molecular Function (MF) O-acyltransferase activity 0.000913 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 0.1201 Highly Informative Inherited
Molecular Function (MF) adenylyltransferase activity 0.02947 Highly Informative Inherited
Cellular Component (CC) protein complex 0.0009626 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.7549 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.3502 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.4767 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0.0002846 Moderately Informative Direct
Cellular Component (CC) actin cytoskeleton 0.00004894 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.0000002426 Informative Direct
Cellular Component (CC) microtubule associated complex 0.0000000001144 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 biosynthesis0.0000002983Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPlastid1Moderately InformativeInherited
Cellular componentKinetochore0.0000002503Highly InformativeDirect
Cellular componentCentromere0.00002121Highly InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionMetal-binding9.203e-16Least 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)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)carbohydrate metabolism0Least InformativeDirect
UniPathway (UP)lipid metabolism0Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)biopolymer biosynthesis0Moderately InformativeDirect
UniPathway (UP)lipid biosynthesis0Moderately InformativeDirect
UniPathway (UP)glycan metabolism0Moderately InformativeDirect
UniPathway (UP)nucleotide metabolism0Moderately InformativeDirect
UniPathway (UP)cellular component biogenesis0Moderately InformativeDirect
UniPathway (UP)membrane lipid metabolism0Moderately InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis0.2437Moderately InformativeInherited
UniPathway (UP)amine and polyamine metabolism1Moderately InformativeInherited
UniPathway (UP)lipopolysaccharide biosynthesis0InformativeDirect
UniPathway (UP)nucleotide-sugar biosynthesis0InformativeDirect
UniPathway (UP)L-lysine biosynthesis0InformativeDirect
UniPathway (UP)carnitine metabolism0.0000000000007922InformativeDirect
UniPathway (UP)glycolipid biosynthesis1InformativeInherited
UniPathway (UP)L-lysine biosynthesis via DAP pathway0Highly InformativeDirect
UniPathway (UP)UDP-N-acetyl-alpha-D-glucosamine biosynthesis0Highly InformativeDirect
UniPathway (UP)glycogen biosynthesis0Highly InformativeDirect
UniPathway (UP)L-cysteine metabolism0Highly 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 ]