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 (1,562) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,953 11,821 8
Proteins 4,865 11,703 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) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.07503 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.119 Moderately Informative Inherited
Cellular Component (CC) protein complex 0.6198 Least Informative Inherited
Cellular Component (CC) membrane 0.7941 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intrinsic component of membrane 0.21 Moderately Informative Inherited
Cellular Component (CC) plasma membrane part 0.1858 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 0.0009923 Informative Direct
Cellular Component (CC) transporter complex 0.00003992 Informative Direct
Cellular Component (CC) integral component of membrane 0.1672 Informative Inherited
Cellular Component (CC) intrinsic component of plasma membrane 0.02617 Informative Inherited
Cellular Component (CC) ion channel complex 0.00001253 Highly Informative Direct
Cellular Component (CC) receptor complex 0.00002291 Highly Informative Direct
Cellular Component (CC) integral component of plasma membrane 0.01862 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)Oxidoreductases0.00001165Least InformativeDirect

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details) Document: MP 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)Oxidoreductases0.00001236Least InformativeDirect
Enzyme Commission (EC)Acting on the CH-NH(2) group of donors0.00000000000001574InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.09184Least InformativeInherited
Biological processElectron transport0.00005752InformativeDirect
Cellular componentCell junction0.000000002368Moderately InformativeDirect
Cellular componentSynapse0.00000000001081InformativeDirect
Cellular componentPeriplasm0.00000006938InformativeDirect
DomainWD repeat0InformativeDirect
Post-translational modificationDevelopmental protein0.0000005147Moderately 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) · Mouse Phenotype (MP) · 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) · Mouse Phenotype (MP) · 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 ]