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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 (3,159) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 27,162 153,614 29
Proteins 26,153 150,595 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 biogenesis0.40781Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.80890.00007683Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.80670.01761Least InformativeInherited
Biological Process (BP)primary metabolic process10.6513Least InformativeInherited
Biological Process (BP)biosynthetic process0.077360.0000000000006791Least InformativeInherited
Biological Process (BP)single-organism cellular process10.6508Least InformativeInherited
Biological Process (BP)macromolecular complex subunit organization0.0089680.3023Moderately InformativeInherited
Biological Process (BP)cellular component assembly0.023880.469Moderately InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.077420.001405Moderately InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.10110.004944Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.065370.09018Moderately InformativeInherited
Biological Process (BP)protein oligomerization0.000030160.0001107InformativeDirect
Biological Process (BP)movement of cell or subcellular component0.016470.5215InformativeInherited
Biological Process (BP)microtubule-based process0.000036990.007302InformativeInherited
Biological Process (BP)sulfur compound biosynthetic process0.027180.0596InformativeInherited
Biological Process (BP)alpha-amino acid biosynthetic process0.0014120.000000007233InformativeInherited
Biological Process (BP)sulfur amino acid metabolic process0.001150.00005211InformativeInherited
Biological Process (BP)microtubule-based movement0.000038830.0001817Highly InformativeDirect
Biological Process (BP)protein homotrimerization0.0000095610.0000008763Highly InformativeDirect
Biological Process (BP)serine family amino acid metabolic process0.002310.0008393Highly InformativeInherited
Molecular Function (MF)transferase activity0.0000045130.00000000000002739Least InformativeDirect
Molecular Function (MF)lyase activity0.025480.1662Moderately InformativeInherited
Molecular Function (MF)transferase activity, transferring acyl groups00InformativeDirect
Molecular Function (MF)hydro-lyase activity0.0000022470.00001247InformativeDirect
Molecular Function (MF)carbonate dehydratase activity0.00010340.000007561Highly InformativeDirect
Molecular Function (MF)O-acyltransferase activity0.000095530.00001385Highly InformativeDirect
Molecular Function (MF)acetyltransferase activity0.0020270.008017Highly InformativeInherited
Cellular Component (CC)non-membrane-bounded organelle0.0060770.7504Least InformativeInherited
Cellular Component (CC)protein complex0.00930.001169Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.074251Least InformativeInherited
Cellular Component (CC)cytoskeleton0.0000015940.009935Moderately InformativeInherited
Cellular Component (CC)microtubule cytoskeleton0.000000017510.0001467InformativeDirect
Cellular Component (CC)actin cytoskeleton0.00036650.00172InformativeInherited

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 0.0000000000006791 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.00007683 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.6508 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.6513 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.01761 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.00000000001379 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00004067 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.3023 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.469 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.9741 Moderately Informative Inherited
Biological Process (BP) response to stress 1 Moderately Informative Inherited
Biological Process (BP) system development 1 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative biosynthetic process 0.02108 Moderately Informative Inherited
Biological Process (BP) organophosphate biosynthetic process 0.399 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.001405 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.02216 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.09018 Moderately Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.004944 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.6415 Moderately Informative Inherited
Biological Process (BP) peptide metabolic process 0.158 Moderately Informative Inherited
Biological Process (BP) gene expression 0.7423 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 0.004571 Moderately Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0.07072 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.4505 Moderately Informative Inherited
Biological Process (BP) sulfur amino acid metabolic process 0.00005211 Informative Direct
Biological Process (BP) polysaccharide metabolic process 0.0000000000001191 Informative Direct
Biological Process (BP) membrane lipid metabolic process 0.0003632 Informative Direct
Biological Process (BP) phospholipid metabolic process 0.0004473 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.00000000000008501 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0.000000002948 Informative Direct
Biological Process (BP) protein oligomerization 0.0001107 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.000000007233 Informative Direct
Biological Process (BP) liposaccharide metabolic process 0.000000002098 Informative Direct
Biological Process (BP) central nervous system development 0.1605 Informative Inherited
Biological Process (BP) cell development 0.9554 Informative Inherited
Biological Process (BP) movement of cell or subcellular component 0.5215 Informative Inherited
Biological Process (BP) microtubule-based process 0.007302 Informative Inherited
Biological Process (BP) sulfur compound biosynthetic process 0.0596 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.002567 Informative Inherited
Biological Process (BP) regulation of cellular amide metabolic process 0.001298 Informative Inherited
Biological Process (BP) energy reserve metabolic process 0.0000005021 Highly Informative Direct
Biological Process (BP) translational initiation 0.000005085 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0.0001817 Highly Informative Direct
Biological Process (BP) serine family amino acid metabolic process 0.0008393 Highly Informative Direct
Biological Process (BP) glycolipid biosynthetic process 0.00003229 Highly Informative Direct
Biological Process (BP) cellular polysaccharide biosynthetic process 0.0000000000234 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 0.0001817 Highly Informative Direct
Biological Process (BP) gliogenesis 0.0001646 Highly Informative Direct
Biological Process (BP) response to drug 0.0006549 Highly Informative Direct
Biological Process (BP) protein homotrimerization 0.0000008763 Highly Informative Direct
Biological Process (BP) oligosaccharide metabolic process 0.07109 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.00000000000002739 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0.1662 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.5715 Moderately Informative Inherited
Molecular Function (MF) molecular function regulator 0.01186 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) hydro-lyase activity 0.00001247 Informative Direct
Molecular Function (MF) RNA binding 0.008817 Informative Inherited
Molecular Function (MF) carbonate dehydratase activity 0.000007561 Highly Informative Direct
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0.0000001502 Highly Informative Direct
Molecular Function (MF) translation factor activity, RNA binding 0.00000002213 Highly Informative Direct
Molecular Function (MF) O-acyltransferase activity 0.00001385 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 0.008017 Highly Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.7504 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.001169 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1542 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0.009935 Moderately Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0.0001467 Informative Direct
Cellular Component (CC) actin cytoskeleton 0.00172 Informative Inherited

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 plant0.01482Least InformativeInherited
Plant ANatomical entity (PAN)root system0.04026Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.1162Least InformativeInherited
Plant ANatomical entity (PAN)leaf0.2298Least InformativeInherited
Plant ANatomical entity (PAN)portion of ground tissue0.000006042InformativeDirect
Plant ANatomical entity (PAN)portion of vascular tissue0.00001815InformativeDirect
Plant ANatomical entity (PAN)fruit0.00003503InformativeDirect
Plant ANatomical entity (PAN)parenchyma cell0.00000000001302Highly InformativeDirect
Plant ANatomical entity (PAN)phloem0.000000004906Highly InformativeDirect
Plant ANatomical entity (PAN)root stele0.0000434Highly 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 phosphorus-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 processLipid A biosynthesis0Highly InformativeDirect
Biological processLysine biosynthesis0Highly InformativeDirect
Biological processPeptidoglycan synthesis0Highly InformativeDirect
Biological processCysteine biosynthesis0.0000003235Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPlastid1Moderately InformativeInherited
Cellular componentKinetochore0.0000007341Highly InformativeDirect
Cellular componentCentromere0.00004299Highly InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionMetal-binding0.0000000000008253Least 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 biosynthesis0.2165Moderately 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 metabolism0.0000000000007096InformativeDirect
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
UniPathway (UP)LPS lipid A biosynthesis0Highly InformativeDirect
UniPathway (UP)starch biosynthesis0.000009589Highly 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 ]