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 (2,809) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 28,102 55,630 44
Proteins 11,524 24,562 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)
Cellular Component (CC)cytoplasmic part0.015690Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.024150.005184Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.014330Least InformativeInherited
Cellular Component (CC)membrane0.015780.09387Least InformativeInherited
Cellular Component (CC)mitochondrial part0.00022470Moderately InformativeDirect
Cellular Component (CC)organelle envelope0.00035256.758e-11Moderately InformativeDirect
Cellular Component (CC)organelle membrane0.00065646.364e-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 9.427e-10 Least Informative Direct
Biological Process (BP) response to stimulus 1 Least Informative Inherited
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 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.6174 Least Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.1163 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.2246 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.3881 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.07408 Moderately Informative Inherited
Biological Process (BP) gene expression 0.549 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.1649 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.04563 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.03988 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.2652 Moderately Informative Inherited
Biological Process (BP) proteolysis 3.651e-10 Informative Direct
Biological Process (BP) mitochondrion organization 2.219e-06 Informative Direct
Biological Process (BP) protein localization to organelle 1.85e-05 Informative Direct
Biological Process (BP) cytoplasmic transport 0.0001472 Informative Direct
Biological Process (BP) protein transport 0.0005019 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 0.0006927 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.00469 Informative Inherited
Biological Process (BP) response to lipid 0.0244 Informative Inherited
Biological Process (BP) phosphorylation 0.008456 Informative Inherited
Biological Process (BP) establishment of protein localization to mitochondrion 8.232e-13 Highly Informative Direct
Biological Process (BP) oxidative phosphorylation 4.078e-11 Highly Informative Direct
Biological Process (BP) mitochondrial transport 5.06e-10 Highly Informative Direct
Biological Process (BP) electron transport chain 3.736e-06 Highly Informative Direct
Biological Process (BP) cellular response to alcohol 1.461e-05 Highly Informative Direct
Biological Process (BP) protein processing 0.5708 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 1.936e-08 Least Informative Direct
Molecular Function (MF) binding 0.7827 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0.324 Moderately Informative Inherited
Molecular Function (MF) transporter activity 0.01894 Moderately Informative Inherited
Molecular Function (MF) cation binding 0.02647 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.225 Moderately Informative Inherited
Molecular Function (MF) peptidase activity 0 Informative Direct
Molecular Function (MF) inorganic cation transmembrane transporter activity 2.83e-05 Informative Direct
Molecular Function (MF) nucleotide binding 0.01935 Informative Inherited
Molecular Function (MF) transition metal ion binding 0.001407 Informative Inherited
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.002798 Informative Inherited
Molecular Function (MF) purine ribonucleoside binding 0.003665 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 8.191e-10 Highly Informative Direct
Molecular Function (MF) ATP binding 0.0003897 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 0.005184 Least Informative Inherited
Cellular Component (CC) protein complex 0.07269 Least Informative Inherited
Cellular Component (CC) membrane 0.09387 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0 Moderately Informative Direct
Cellular Component (CC) organelle envelope 6.758e-11 Moderately Informative Direct
Cellular Component (CC) organelle membrane 6.364e-07 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.5612 Moderately Informative Inherited
Cellular Component (CC) respiratory chain 4.327e-10 Informative Direct
Cellular Component (CC) mitochondrial matrix 3.429e-07 Informative Direct
Cellular Component (CC) mitochondrial membrane part 7.866e-06 Informative Direct
Cellular Component (CC) mitochondrial respiratory chain 0.0003035 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

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

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
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)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least 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)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately 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 processTransport0.9352Least InformativeInherited
Biological processElectron transport2.481e-10InformativeDirect
Biological processRespiratory chain0Highly InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentPeriplasm2.171e-05InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Post-translational modificationHydrolase1.09e-12Least 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]