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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 (1,568) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 4,978 24,968 8
Proteins 4,888 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) single-organism cellular process 0.3327 Least Informative Inherited
Biological Process (BP) biological regulation 0.7794 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.0000001611 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0.000936 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.00048 Moderately Informative Direct
Biological Process (BP) cellular developmental process 0.0000009248 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.000001726 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.00003282 Moderately Informative Direct
Biological Process (BP) system development 0.01267 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.08295 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.2043 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.003957 Moderately Informative Inherited
Biological Process (BP) animal organ morphogenesis 0.0000009178 Informative Direct
Biological Process (BP) tissue development 0.00005447 Informative Direct
Biological Process (BP) positive regulation of gene expression 0.000003194 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.0000009077 Informative Direct
Biological Process (BP) regulation of cell differentiation 0.00000003298 Informative Direct
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.0000009011 Informative Direct
Biological Process (BP) positive regulation of developmental process 0.000000002503 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 0.00000003554 Informative Direct
Biological Process (BP) circulatory system development 0.000003049 Informative Direct
Cellular Component (CC) cell projection 0.02351 Moderately Informative Inherited
Cellular Component (CC) plasma membrane bounded cell projection part 0.0004661 Informative Direct
Cellular Component (CC) neuron projection 0.1544 Informative Inherited
Cellular Component (CC) growth cone 0.00001011 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

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect
Yeast Phenotype (YP)metabolism and growth0Least InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA 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)Oxidoreductases0.00001095Least InformativeDirect
Enzyme Commission (EC)Acting on the CH-NH(2) group of donors0.000000000000007728InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.02271Least InformativeInherited
Biological processElectron transport0.0005346InformativeDirect
Cellular componentCell junction0.00000001491Moderately InformativeDirect
Cellular componentCell projection0.00000002013Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.000004996Moderately InformativeDirect
Cellular componentSynapse0.00000000004267InformativeDirect
Cellular componentPeriplasm0.0000001549InformativeDirect
DomainWD repeat0InformativeDirect
Post-translational modificationDevelopmental protein0.000001077Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect

Document: UP 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) · Fly Phenotype (FP) · Fly Anatomy (FA) · 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 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) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]