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Alanine racemase C-terminal domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Domain of alpha and beta subunits of F1 ATP synthase-like [ 50614] (3)
Superfamily:   Alanine racemase C-terminal domain-like [ 50621] (2)
Families:   Alanine racemase [ 88682]
  Eukaryotic ODC-like [ 88683] (2)


Superfamily statistics
Genomes (2,947) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 8,929 53,589 18
Proteins 8,887 53,490 15


Functional annotation
General category Metabolism
Detailed category Amino acids 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) biosynthetic process 0.000000001422 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0002166 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.000000000006862 Least Informative Direct
Biological Process (BP) biological regulation 0.9796 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.01526 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.6078 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.000000000001076 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.0000006969 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.04484 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.02451 Moderately Informative Inherited
Biological Process (BP) amine metabolic process 0 Informative Direct
Biological Process (BP) regulation of catabolic process 0.000000000000009084 Informative Direct
Biological Process (BP) regulation of transmembrane transport 0.0000001817 Informative Direct
Biological Process (BP) positive regulation of transport 0.0002913 Informative Direct
Biological Process (BP) ammonium ion metabolic process 0 Informative Direct
Biological Process (BP) polyamine metabolic process 0 Highly Informative Direct
Biological Process (BP) negative regulation of catabolic process 0.00000004682 Highly Informative Direct
Biological Process (BP) positive regulation of transmembrane transport 0.0000000007344 Highly Informative Direct
Biological Process (BP) regulation of protein catabolic process 0 Highly Informative Direct
Biological Process (BP) cellular biogenic amine biosynthetic process 0.000000003916 Highly Informative Direct
Molecular Function (MF) binding 0.9691 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0.00001651 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.0001097 Moderately Informative Direct
Molecular Function (MF) anion binding 0.0003962 Moderately Informative Direct
Molecular Function (MF) molecular function regulator 0.00005724 Moderately Informative Direct
Molecular Function (MF) enzyme activator activity 0.000000005633 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0 Informative Direct
Molecular Function (MF) racemase and epimerase activity 0.000000000000006264 Informative Direct
Molecular Function (MF) identical protein binding 0.000001042 Informative Direct
Molecular Function (MF) protein dimerization activity 0.0000002406 Informative Direct
Molecular Function (MF) carboxy-lyase activity 0 Highly Informative Direct
Molecular Function (MF) vitamin binding 0.0000000000002368 Highly Informative Direct
Molecular Function (MF) protein homodimerization activity 0.000000006255 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.7038 Least Informative Inherited
Cellular Component (CC) perinuclear region of cytoplasm 0.0001482 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)Lyases0Least InformativeDirect
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Racemases and epimerases0Moderately InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on amino acids and derivatives0InformativeDirect
Enzyme Commission (EC)Arginine decarboxylase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0.0211Moderately InformativeInherited
Biological processPolyamine biosynthesis0Highly InformativeDirect
Biological processLysine biosynthesis0Highly InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationDecarboxylase0Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009006 SSF50621 Protein matches
Abstract

This entry represents a beta-barrel domain found at the C-terminal of alanine racemase and in group IV pyridoxal-5'-phosphate (PLP)-dependent decarboxylases, such as eukaryotic ornithine decarboxylase , arginine decarboxylase and diaminopimelate decarboxylase . These enzymes belong to the same structural family.

Alanine racemase plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine. Proteins contains this domain are found in both prokaryotic and eukaryotic proteins [PubMed1676385,PubMed7871888]. The molecular structure of alanine racemase from Bacillus stearothermophilus was determined by X-ray crystallography to a resolution of 1.9 A [PubMed9063881]. The alanine racemase monomer is composed of two domains, an eight-stranded alpha/beta barrel at the N-terminus, and a C-terminal domain essentially composed of beta-strand. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above the mouth of the alpha/beta barrel and is covalently linked via an aldimine linkage to a lysine residue, which is at the C-terminus of the first beta-strand of the alpha/beta barrel.

Eukaryotic ornithine decarboxylase (ODC) acts as a homodimer to produce putrescine (1,4-diaminobutane) from ornithine, where putrescine is the precursor of other polyamines in animals, plants, and bacteria. Arginine decarboxylase is also involved in putrescine biosynthesis. This is the first committed step in polyamine biosynthesis. Alanine racemase is a structurally homologous enzyme. Both proteins share a common alpha/beta barrel that binds the cofactor via a Schiff base on the C-terminal end of the barrel [PubMed10378276].

Diaminopimelate decarboxylase (DapDC) catalyzes the final step of lysine biosynthesis in bacteria.


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 8 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 Alanine racemase C-terminal domain-like 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 8 hidden Markov models representing the Alanine racemase C-terminal domain-like 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 ]