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LuxS/MPP-like metallohydrolase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   LuxS/MPP-like metallohydrolase [ 63410]
Superfamily:   LuxS/MPP-like metallohydrolase [ 63411] (2)
Families:   Autoinducer-2 production protein LuxS [ 64294]
  MPP-like [ 63412] (6)


Superfamily statistics
Genomes (2,859) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 29,136 139,866 44
Proteins 11,987 59,765 23


Functional annotation
General category Processes_IC
Detailed category Proteases

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)multi-organism process0.00029020.7474Moderately InformativeInherited
Biological Process (BP)multi-organism cellular process0.000000010820.0000627Highly 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) organonitrogen compound metabolic process 0.00000000000005866 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.002413 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.9883 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.8385 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.05669 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.6938 Least Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0.000000539 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.0009391 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.0005643 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.0002807 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.0003856 Moderately Informative Direct
Biological Process (BP) nitrogen compound transport 0.00003636 Moderately Informative Direct
Biological Process (BP) cellular localization 0.002388 Moderately Informative Inherited
Biological Process (BP) purine-containing compound metabolic process 0.005239 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.7474 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.23 Moderately Informative Inherited
Biological Process (BP) gene expression 0.02511 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.1179 Moderately Informative Inherited
Biological Process (BP) proteolysis 0 Informative Direct
Biological Process (BP) mitochondrion organization 0.00000000002766 Informative Direct
Biological Process (BP) protein transport 0.000000373 Informative Direct
Biological Process (BP) electron transport chain 0.00000001129 Informative Direct
Biological Process (BP) protein localization to organelle 0.000000001378 Informative Direct
Biological Process (BP) cellular respiration 0.0000001568 Informative Direct
Biological Process (BP) ATP metabolic process 0.000001252 Informative Direct
Biological Process (BP) intracellular transport 0.00003095 Informative Direct
Biological Process (BP) phosphorylation 0.02652 Informative Inherited
Biological Process (BP) protein targeting 0.00000000000001422 Highly Informative Direct
Biological Process (BP) mitochondrial transport 0 Highly Informative Direct
Biological Process (BP) multi-organism cellular process 0.0000627 Highly Informative Direct
Biological Process (BP) protein maturation 0 Highly Informative Direct
Biological Process (BP) establishment of protein localization to mitochondrion 0 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.00000000000009963 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0.5548 Moderately Informative Inherited
Molecular Function (MF) transporter activity 0.01962 Moderately Informative Inherited
Molecular Function (MF) metal ion binding 0.02578 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.1398 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.378 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.0475 Moderately Informative Inherited
Molecular Function (MF) zinc ion binding 0.0001841 Informative Direct
Molecular Function (MF) monovalent inorganic cation transmembrane transporter activity 0.0000002992 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.01023 Informative Inherited
Molecular Function (MF) ribonucleotide binding 0.01145 Informative Inherited
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.005267 Informative Inherited
Molecular Function (MF) peptidase activity, acting on L-amino acid peptides 0.7512 Informative Inherited
Molecular Function (MF) ATP binding 0.0008976 Highly Informative Direct
Molecular Function (MF) metallopeptidase activity 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000004008 Least Informative Direct
Cellular Component (CC) protein complex 0.000004202 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.001001 Least Informative Inherited
Cellular Component (CC) membrane 0.06156 Least Informative Inherited
Cellular Component (CC) organelle inner membrane 0 Moderately Informative Direct
Cellular Component (CC) membrane protein complex 0.00001457 Moderately Informative Direct
Cellular Component (CC) mitochondrial protein complex 0 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0.003894 Moderately Informative Inherited
Cellular Component (CC) mitochondrial envelope 0.02716 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.00366 Moderately Informative Inherited
Cellular Component (CC) mitochondrial respiratory chain 0.000005313 Informative Direct
Cellular Component (CC) plastid 0.0002601 Informative Direct
Cellular Component (CC) cytochrome complex 0.00000000004298 Informative Direct
Cellular Component (CC) inner mitochondrial membrane protein complex 0.0006906 Informative Direct
Cellular Component (CC) respiratory chain complex 0.0000003473 Informative Direct
Cellular Component (CC) oxidoreductase complex 0.000000000001913 Informative Direct
Cellular Component (CC) transporter complex 0.0000000002448 Informative Direct
Cellular Component (CC) mitochondrial respiratory chain complex III 0.000000000003125 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)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Metalloendopeptidases0InformativeDirect
Enzyme Commission (EC)Carbon-sulfur lyases1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processElectron transport0.000000005669InformativeDirect
Biological processRespiratory chain0Highly InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentPeriplasm0.00003007InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Post-translational modificationHydrolase4.413e-16Least InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationMetalloprotease0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011249 SSF63411 Protein matches
Abstract

This entry represents domains with a two-layer alpha/beta structure found in metalloenzymes such as LuxS (S-ribosylhomocysteinase) and metallopeptidases belonging to MEROPS peptidase family M16. These domains share the same active site motif of HxxEH located in the first core helix, but differ in one of the metal-binding residues. LuxS, the AI-2 (autoinducer-2) producing enzyme for quorum sensing in bacteria, is a homodimeric iron-dependent metalloenzyme containing two identical tetrahedral metal-binding sites similar to those found in peptidases and amidases, although it contains an extra N-terminal strand [PubMed15751951, PubMed11553770]. Some M16 family metallopeptidases, such as mitochondrial processing peptidase (MPP), share the same common fold elaborated with many extra additional structures [PubMed11470436]. These peptidases usually contain a duplication of this domain, although only the N-terminal domain binds the catalytic metal.


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) · UniProtKB KeyWords (KW) ]

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 28 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 LuxS/MPP-like metallohydrolase 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 28 hidden Markov models representing the LuxS/MPP-like metallohydrolase 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) · UniProtKB KeyWords (KW) · Internal database links ]