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 (2,851) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 28,899 118,763 44
Proteins 11,881 54,569 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)single-organism metabolic process0.066520.9996Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.0088110.5355Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.021341Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.012621Least InformativeInherited
Biological Process (BP)single-organism cellular process0.55641Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.0086280.6578Least InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process0.00023290.00003368Moderately InformativeDirect
Biological Process (BP)carbohydrate derivative metabolic process0.00055190.1177Moderately InformativeInherited
Biological Process (BP)purine ribonucleoside metabolic process0.000023470.000002322InformativeDirect
Cellular Component (CC)intracellular organelle part0.086390.033Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.0048620Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.0052190Least InformativeInherited
Cellular Component (CC)membrane0.031660.1408Least InformativeInherited
Cellular Component (CC)mitochondrial part0.00080710Moderately InformativeDirect
Cellular Component (CC)organelle envelope0.0012490.0000000002206Moderately InformativeInherited

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 0.0000003342 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.9996 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) localization 0.252 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.6578 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.5355 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.7898 Least Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.00003368 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.000001174 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.1475 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.4557 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.1773 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.3831 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.03963 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.1279 Moderately Informative Inherited
Biological Process (BP) gene expression 0.7684 Moderately Informative Inherited
Biological Process (BP) ion transport 0.1934 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.08984 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.215 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.1177 Moderately Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0.000002322 Informative Direct
Biological Process (BP) proteolysis 0.00000000009373 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 0.0000000005167 Informative Direct
Biological Process (BP) protein maturation 0.0000004313 Informative Direct
Biological Process (BP) monovalent inorganic cation transport 0.000003018 Informative Direct
Biological Process (BP) mitochondrion organization 0.000003294 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 0.00002363 Informative Direct
Biological Process (BP) protein localization to organelle 0.00002725 Informative Direct
Biological Process (BP) ion transmembrane transport 0.0001135 Informative Direct
Biological Process (BP) cytoplasmic transport 0.0002952 Informative Direct
Biological Process (BP) protein transport 0.0007069 Informative Direct
Biological Process (BP) response to lipid 0.04614 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.006702 Informative Inherited
Biological Process (BP) phosphorylation 0.0143 Informative Inherited
Biological Process (BP) nucleoside triphosphate metabolic process 0.02233 Informative Inherited
Biological Process (BP) nucleoside monophosphate metabolic process 0.002024 Informative Inherited
Biological Process (BP) single-organism cellular localization 0.00221 Informative Inherited
Biological Process (BP) single-organism intracellular transport 0.05609 Informative Inherited
Biological Process (BP) protein localization to mitochondrion 0.000000000002339 Highly Informative Direct
Biological Process (BP) electron transport chain 0.000000000006587 Highly Informative Direct
Biological Process (BP) oxidative phosphorylation 0.000000000008081 Highly Informative Direct
Biological Process (BP) mitochondrial transport 0.0000000008102 Highly Informative Direct
Biological Process (BP) hydrogen ion transmembrane transport 0.0000000008414 Highly Informative Direct
Biological Process (BP) response to alcohol 0.00451 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.000000001085 Least Informative Direct
Molecular Function (MF) binding 0.9369 Least Informative Inherited
Molecular Function (MF) small molecule binding 0.07143 Moderately Informative Inherited
Molecular Function (MF) transporter activity 0.02461 Moderately Informative Inherited
Molecular Function (MF) cation binding 0.03961 Moderately Informative Inherited
Molecular Function (MF) oxidoreductase activity 0.3434 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.04327 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.2165 Moderately Informative Inherited
Molecular Function (MF) peptidase activity 0 Informative Direct
Molecular Function (MF) monovalent inorganic cation transmembrane transporter activity 0.000001193 Informative Direct
Molecular Function (MF) zinc ion binding 0.00006896 Informative Direct
Molecular Function (MF) nucleotide binding 0.02602 Informative Inherited
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.003958 Informative Inherited
Molecular Function (MF) purine ribonucleoside binding 0.005103 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 0.000000001097 Highly Informative Direct
Molecular Function (MF) ATP binding 0.0005824 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) protein complex 0.0571 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.033 Least Informative Inherited
Cellular Component (CC) membrane 0.1408 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.0000000002206 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0.03746 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.622 Moderately Informative Inherited
Cellular Component (CC) respiratory chain 0.00000000002513 Informative Direct
Cellular Component (CC) oxidoreductase complex 0.000000001151 Informative Direct
Cellular Component (CC) transporter complex 0.00000004409 Informative Direct
Cellular Component (CC) mitochondrial matrix 0.000000138 Informative Direct
Cellular Component (CC) mitochondrial membrane part 0.0000008201 Informative Direct
Cellular Component (CC) integral component of membrane 0.02458 Informative Inherited

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 variant0.0000293Moderately InformativeDirect
Worm Phenotype (WP)basement membrane remodeling variant0.00001202InformativeDirect

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 processTransport0.9432Least InformativeInherited
Biological processElectron transport0.0000000002657InformativeDirect
Biological processRespiratory chain0Highly InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentPeriplasm0.00002302InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Post-translational modificationHydrolase0.0000000000009353Least 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) · Yeast Phenotype (YP) · 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) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]