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RmlC-like cupins superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Double-stranded beta-helix [ 51181] (7)
Superfamily:   RmlC-like cupins [ 51182] (24)
Families:   dTDP-sugar isomerase [ 51183] (4)
  Glucose-6-phosphate isomerase, GPI [ 89403]
  Hypothetical protein TM1112 [ 89406]
  TM1287-like [ 89409] (4)
  TM1459-like [ 101976] (2)
  Germin/Seed storage 7S protein [ 51187] (4)
  YlbA-like [ 101979] (4)
  Pirin-like [ 101984] (2)
  Quercetin 2,3-dioxygenase-like [ 75035] (2)
  Type I phosphomannose isomerase [ 51191] (3)
  Homogentisate dioxygenase [ 51194]
  Acireductone dioxygenase [ 82191]
  KduI-like [ 110318]
  Ureidoglycolate hydrolase AllA [ 117312]
  Probable transcriptional regulator VC1968, C-terminal domain [ 117315]
  YML079-like [ 117318] (3)
  PA5104-like [ 141609]
  MJ0764-like [ 141612]
  Cysteine dioxygenase type I [ 141615]
  3-hydroxyanthranilic acid dioxygenase-like [ 141618]
  Acetylacetone-cleaving enzyme-like [ 159293]
  VPA0057-like [ 159296]
  Gentisate 1,2-dioxygenase-like [ 159299]
  EutQ-like [ 159304]


Superfamily statistics
Genomes (2,953) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 45,244 357,470 90
Proteins 44,557 353,260 84


Functional annotation
General category Metabolism
Detailed category Nitrogen metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Lyases0.5417Least InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases1Least InformativeInherited
Enzyme Commission (EC)Intramolecular oxidoreductases0Moderately InformativeDirect
Enzyme Commission (EC)Hydro-lyases0.000002917Moderately InformativeDirect
Enzyme Commission (EC)Racemases and epimerases1Moderately InformativeInherited
Enzyme Commission (EC)Carboxy-lyases0.8946Moderately InformativeInherited
Enzyme Commission (EC)Acting on single donors with incorporation of mole0InformativeDirect
Enzyme Commission (EC)Interconverting aldoses and ketoses, and related c0InformativeDirect
Enzyme Commission (EC)Acting on carbohydrates and derivatives0.0000005017InformativeDirect
Enzyme Commission (EC)In linear amidines0Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details) Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details) 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)trunk0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)seed development stage0.0001456InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Lyases0.0005566Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Glycosyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0.9551Moderately InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds1Moderately InformativeInherited
Enzyme Commission (EC)Carbon-carbon lyases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on single donors with incorporation of molecular oxygen (oxygenases). The oxygen incorporated0InformativeDirect
Enzyme Commission (EC)Pentosyltransferases0InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0InformativeDirect
Enzyme Commission (EC)Carbon-nitrogen lyases2.515e-16InformativeDirect
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors1InformativeInherited
Enzyme Commission (EC)Racemases and epimerases1InformativeInherited
Enzyme Commission (EC)With incorporation of two atoms of oxygen0Highly InformativeDirect
Enzyme Commission (EC)Lyases acting on amides, amidines, etc0Highly InformativeDirect
Enzyme Commission (EC)Interconverting aldoses and ketoses0.0000002611Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0.0000006515Highly InformativeDirect
Enzyme Commission (EC)Acting on carbohydrates and derivatives0.000001224Highly InformativeDirect
Enzyme Commission (EC)In linear amidines0.164Highly InformativeInherited
Enzyme Commission (EC)Carbon-sulfur lyases1Highly InformativeInherited
Enzyme Commission (EC)Transposing C=C bonds1Highly InformativeInherited

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR011051 SSF51182 Protein matches
Abstract

RmlC (dTDP (deoxythimodone diphosphates)-4-dehydrorhamnose 3,5-epimerase) is a dTDP-sugar isomerase enzyme involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria [PubMed10802738]. RmlC is a dimer, each monomer being formed from two beta-sheets arranged in a beta-sandwich, where the substrate-binding site is located between the two sheets of both monomers.

Other protein families contain domains that share this fold, including glucose-6-phosphate isomerase ; germin, a metal-binding protein with oxalate oxidase and superoxide dismutases activities [PubMed11062559]; auxin-binding protein [PubMed12065401]; seed storage protein 7S [PubMed11124907]; acireductone dioxygenase [PubMed12402029]; as well as three proteins that have metal-binding sites similar to that of germine, namely quercetin 2,3-dioxygenase [PubMed11839311], phosphomannose isomerase [PubMed8612079] and homogentisate dioxygenase [PubMed10876237], the last three sharing a 2-domain fold with storage protein 7s.


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 · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

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 68 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 RmlC-like cupins 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 68 hidden Markov models representing the RmlC-like cupins 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]