SUPERFAMILY 1.75 HMM library and genome assignments server


YVTN repeat-like/Quinoprotein amine dehydrogenase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   7-bladed beta-propeller [ 50964] (14)
Superfamily:   YVTN repeat-like/Quinoprotein amine dehydrogenase [ 50969] (3)
Families:   YVTN repeat [ 82166]
  Quinohemoprotein amine dehydrogenase B chain [ 69309]
  Methylamine dehydrogenase, H-chain [ 50970]


Superfamily statistics
Genomes (1,515) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 4,713 7,022 8
Proteins 4,631 6,926 8


Functional annotation
General category Metabolism
Detailed category Other enzymes

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Cellular Component (CC) protein complex 0.6282 Least Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) intrinsic to membrane 0.2012 Moderately Informative Inherited
Cellular Component (CC) plasma membrane part 0.2847 Moderately Informative Inherited
Cellular Component (CC) integral to membrane 0.1595 Informative Inherited
Cellular Component (CC) intrinsic to plasma membrane 0.0254 Informative Inherited
Cellular Component (CC) ion channel complex 1.242e-05 Highly Informative Direct
Cellular Component (CC) receptor complex 1.998e-05 Highly Informative Direct
Cellular Component (CC) integral to plasma membrane 0.01804 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases1.165e-05Least InformativeDirect

Document: EC annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases1.305e-05Least InformativeDirect
Enzyme Commission (EC)Acting on the CH-NH(2) group of donors1.729e-14InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.09147Least InformativeInherited
Biological processElectron transport5.878e-05InformativeDirect
Cellular componentCell junction2.181e-09Moderately InformativeDirect
Cellular componentSynapse9.016e-12InformativeDirect
Cellular componentPeriplasm7.059e-08InformativeDirect
DomainWD repeat0InformativeDirect
Post-translational modificationDevelopmental protein5.265e-07Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011044 SSF50969 Protein matches
Abstract

Quinohemoprotein amine dehydrogenase (QHNDH) from Paracoccus denitrificans is a heterotrimer consisting of alpha, beta and gamma chains [PubMed11717396]. The alpha chain has a four-domain structure that includes a dihaem cytochrome c, the beta chain forms a 7-bladed beta-propeller that is part of the enzyme active site, and the gamma chain contains the redox factor cysteine tryptophylquinone (CTQ).

The beta chain of QHNDH structurally resembles the 7-bladed beta propeller of the H chain of the periplasmic quinoprotein methylamine dehydrogenase (MADH), found in methylotrophic bacteria [PubMed9514722]. MADH is a heterotetramer consisting of two heavy (H) chains and two light (L) chains, and contains the redox cofactor tryptophan tryptophylquinone (TTQ). There is no similarity between the quinone-containing chains of MAD and QHNDH.

The beta-propeller structure found in MAD and QHNDH is similar to the YVTN (Tyr-Val-Thr-Asn) repeat that folds into a beta-propeller found in the N-terminal domain of archaeal surface layer proteins, which help protect cells from extreme environments [PubMed12377130].


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-coverage) · Enzyme Commission (EC) · 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 6 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 YVTN repeat-like/Quinoprotein amine dehydrogenase 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 6 hidden Markov models representing the YVTN repeat-like/Quinoprotein amine dehydrogenase 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-coverage) · Enzyme Commission (EC) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]