SUPERFAMILY 1.75 HMM library and genome assignments server


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 (2,194) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 23,643 55,630 44
Proteins 9,608 24,562 23


Functional annotation
General category Processes_IC
Detailed category Proteases

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

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GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Cellular Component (CC)cytoplasmic part0.0053180Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.025880.01483Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.0052310Least InformativeInherited
Cellular Component (CC)membrane0.0077620.1774Least InformativeInherited
Cellular Component (CC)mitochondrial part0.00024180Moderately InformativeDirect
Cellular Component (CC)organelle envelope0.00040982.069e-10Moderately InformativeDirect
Cellular Component (CC)organelle membrane0.00051283.375e-07Moderately 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) protein metabolic process 1.091e-09 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) localization 0.9784 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.5806 Least Informative Inherited
Biological Process (BP) oxidation-reduction process 1.338e-07 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0.02928 Moderately Informative Inherited
Biological Process (BP) gene expression 0.603 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.1299 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.03712 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.03241 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.2054 Moderately Informative Inherited
Biological Process (BP) proteolysis 7.109e-10 Informative Direct
Biological Process (BP) mitochondrion organization 1.419e-06 Informative Direct
Biological Process (BP) protein localization to organelle 1.261e-05 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 3.287e-05 Informative Direct
Biological Process (BP) cytoplasmic transport 0.0001433 Informative Direct
Biological Process (BP) protein transport 0.000441 Informative Direct
Biological Process (BP) establishment of protein localization to mitochondrion 8.302e-13 Highly Informative Direct
Biological Process (BP) oxidative phosphorylation 4.437e-12 Highly Informative Direct
Biological Process (BP) mitochondrial transport 3.523e-10 Highly Informative Direct
Biological Process (BP) respiratory electron transport chain 0.004041 Highly Informative Inherited
Biological Process (BP) protein processing 0.6024 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 8.521e-10 Least Informative Direct
Molecular Function (MF) binding 0.8094 Least Informative Inherited
Molecular Function (MF) heterocyclic compound binding 1 Moderately Informative Inherited
Molecular Function (MF) organic cyclic compound binding 1 Moderately Informative Inherited
Molecular Function (MF) oxidoreductase activity 0.7329 Moderately Informative Inherited
Molecular Function (MF) transporter activity 0.1913 Moderately Informative Inherited
Molecular Function (MF) cation binding 0.02495 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.2326 Moderately Informative Inherited
Molecular Function (MF) peptidase activity 0 Informative Direct
Molecular Function (MF) nucleotide binding 0.02245 Informative Inherited
Molecular Function (MF) inorganic cation transmembrane transporter activity 0.00255 Informative Inherited
Molecular Function (MF) transition metal ion binding 0.001237 Informative Inherited
Molecular Function (MF) endopeptidase activity 0 Highly Informative Direct
Molecular Function (MF) metallopeptidase activity 0 Highly Informative Direct
Molecular Function (MF) hydrogen ion transmembrane transporter activity 1.708e-07 Highly Informative Direct
Molecular Function (MF) zinc ion binding 4.134e-05 Highly Informative Direct
Molecular Function (MF) ATP binding 0.0006559 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.01483 Least Informative Inherited
Cellular Component (CC) membrane 0.1774 Least Informative Inherited
Cellular Component (CC) protein complex 0.03768 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0 Moderately Informative Direct
Cellular Component (CC) organelle envelope 2.069e-10 Moderately Informative Direct
Cellular Component (CC) organelle membrane 3.375e-07 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.8588 Moderately Informative Inherited
Cellular Component (CC) respiratory chain 1.815e-13 Informative Direct
Cellular Component (CC) mitochondrial membrane part 1.914e-05 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

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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

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)pericellular component development variant2.93e-05Moderately InformativeDirect
Worm Phenotype (WP)basement membrane remodeling variant1.202e-05InformativeDirect

Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

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XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male genitalia0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)intestine0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ovary0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)heart0InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

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AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)shoot apex0Least InformativeDirect
Plant ANatomical entity (PAN)plant embryo0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)vascular leaf0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)sepal0Least InformativeDirect
Plant ANatomical entity (PAN)petal0Least InformativeDirect
Plant ANatomical entity (PAN)stem0Least InformativeDirect
Plant ANatomical entity (PAN)androecium0Least InformativeDirect
Plant ANatomical entity (PAN)leaf lamina0Least InformativeDirect
Plant ANatomical entity (PAN)collective leaf structure0Least InformativeDirect
Plant ANatomical entity (PAN)stalk0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Moderately 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 processTransport0.9377Least InformativeInherited
Biological processElectron transport2.707e-10InformativeDirect
Biological processRespiratory chain0Highly InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentPeriplasm2.112e-05InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Post-translational modificationHydrolase3.033e-12Least InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationMetalloprotease0InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)cofactor metabolism0Least InformativeDirect
UniPathway (UP)quinone cofactor biosynthesis0InformativeDirect
UniPathway (UP)pyrroloquinoline quinone biosynthesis0Highly InformativeDirect

Document: UP 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) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · 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 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) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]