SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 (1,570) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 4,990 24,968 8
Proteins 4,900 24,633 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)
Biological Process (BP) multicellular organismal process 0.0004585 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.192 Least Informative Inherited
Biological Process (BP) biological regulation 0.6552 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.00000001286 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.00000003236 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.00000005355 Moderately Informative Direct
Biological Process (BP) tissue development 0.000002906 Moderately Informative Direct
Biological Process (BP) animal organ development 0.0000157 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.00002243 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.00004283 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0.0005526 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.07539 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.152 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.006874 Moderately Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.000000006573 Informative Direct
Biological Process (BP) regulation of cell differentiation 0.00000001672 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 0.0000001045 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.0000001246 Informative Direct
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.0000003529 Informative Direct
Biological Process (BP) animal organ morphogenesis 0.0000004716 Informative Direct
Biological Process (BP) positive regulation of gene expression 0.0000006277 Informative Direct
Biological Process (BP) circulatory system development 0.000001333 Informative Direct
Biological Process (BP) heart development 0.00000000006487 Highly Informative Direct
Cellular Component (CC) cell projection 0.03296 Moderately Informative Inherited
Cellular Component (CC) plasma membrane bounded cell projection part 0.0006632 Informative Direct
Cellular Component (CC) neuron projection 0.1677 Informative Inherited
Cellular Component (CC) growth cone 0.000009721 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)Oxidoreductases0.00001165Least InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.02598Least InformativeInherited
Biological processElectron transport0.0005234InformativeDirect
Cellular componentCell junction0.00000001869Moderately InformativeDirect
Cellular componentCell projection0.00000002634Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.000006098Moderately InformativeDirect
Cellular componentSynapse0.00000000005063InformativeDirect
Cellular componentPeriplasm0.0000001804InformativeDirect
DomainWD repeat0InformativeDirect
Post-translational modificationDevelopmental protein0.00000125Moderately 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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]