SUPERFAMILY 1.75 HMM library and genome assignments server

Substrate-binding domain of HMG-CoA reductase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Substrate-binding domain of HMG-CoA reductase [ 56541]
Superfamily:   Substrate-binding domain of HMG-CoA reductase [ 56542]
Families:   Substrate-binding domain of HMG-CoA reductase [ 56543]


Superfamily statistics
Genomes (1,146) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,653 7,798 2
Proteins 1,637 7,775 2


Functional annotation
General category Metabolism
Detailed category Coenzyme metabolism and transport

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 metabolic process 0.000000006575 Least Informative Direct
Biological Process (BP) biosynthetic process 0.000001031 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0004959 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.05383 Least Informative Inherited
Biological Process (BP) response to stimulus 0.0602 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.03829 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.201 Least Informative Inherited
Biological Process (BP) lipid metabolic process 0 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of phosphorus metabolic process 0.000003988 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.00002534 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.00004649 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.00016 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.0002062 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.000459 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.001177 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.003343 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.008981 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.02953 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.08351 Moderately Informative Inherited
Biological Process (BP) alcohol metabolic process 0 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 0.00000000007566 Informative Direct
Biological Process (BP) regulation of MAPK cascade 0.0000000007435 Informative Direct
Biological Process (BP) negative regulation of catalytic activity 0.0000001076 Informative Direct
Biological Process (BP) response to light stimulus 0.0000003945 Informative Direct
Biological Process (BP) negative regulation of cellular protein metabolic process 0.0000004381 Informative Direct
Biological Process (BP) regulation of transferase activity 0.000001006 Informative Direct
Biological Process (BP) negative regulation of signaling 0.000002282 Informative Direct
Biological Process (BP) neurological system process 0.000002964 Informative Direct
Biological Process (BP) isoprenoid metabolic process 0.000003836 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.000004617 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 0.000007619 Informative Direct
Biological Process (BP) single-organism behavior 0.00000974 Informative Direct
Biological Process (BP) phospholipid metabolic process 0.0001731 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 0.1955 Informative Inherited
Biological Process (BP) sterol metabolic process 0 Highly Informative Direct
Biological Process (BP) steroid biosynthetic process 0.0000000000002315 Highly Informative Direct
Biological Process (BP) negative regulation of transferase activity 0.00000000036 Highly Informative Direct
Biological Process (BP) negative regulation of protein phosphorylation 0.0000000007278 Highly Informative Direct
Biological Process (BP) learning or memory 0.00000000244 Highly Informative Direct
Biological Process (BP) regulation of protein serine/threonine kinase activity 0.00000001236 Highly Informative Direct
Biological Process (BP) isoprenoid biosynthetic process 0.00000002545 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular signal transduction 0.0001962 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on CH-OH group of donors 0 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 0 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.08126 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.2068 Least Informative Inherited
Cellular Component (CC) membrane 0.05244 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1742 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.00001531 Moderately Informative Direct
Cellular Component (CC) membrane region 0.00001925 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0.1282 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum membrane 0.00000009442 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0Moderately InformativeDirect
Enzyme Commission (EC)Hydroxymethylglutaryl-CoA reductase (NADPH)0Highly InformativeDirect

Document: EC 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)Acting on the CH-OH group of donors0Moderately InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processLipid metabolism0Moderately InformativeDirect
Biological processLipid biosynthesis0InformativeDirect
Biological processSteroid metabolism0InformativeDirect
Biological processIsoprene biosynthesis0Highly InformativeDirect
Biological processSteroid biosynthesis0Highly InformativeDirect
Biological processSterol biosynthesis0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
DomainTransmembrane0Least InformativeDirect
Molecular functionNADP0InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationIsopeptide bond0.0000007846Moderately InformativeDirect
Post-translational modificationUbl conjugation0.0003213Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)metabolic intermediate biosynthesis0Moderately InformativeDirect
UniPathway (UP)(R)-mevalonate metabolism0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR009029 SSF56542 Protein matches
Abstract

This entry represents the substrate-binding L-domain found in class I and II enzymes. The L-domain has the same structural fold in both classes of enzymes, and is unique to HMG-CoA reductases. Its topology resembles a prism, with a central alpha helix surrounded by three alpha/beta subdomains forming three roughly triangular walls [PubMed10698924, PubMed10377386].


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) · 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 2 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 Substrate-binding domain of HMG-CoA reductase 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 2 hidden Markov models representing the Substrate-binding domain of HMG-CoA reductase 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) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]