SUPERFAMILY 1.75 HMM library and genome assignments server


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 (2,938) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 8,883 56,746 18
Proteins 8,841 56,657 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) nitrogen compound metabolic process 4.499e-13 Least Informative Direct
Biological Process (BP) biosynthetic process 2.111e-05 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0003199 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.02253 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 1.931e-15 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 1.783e-06 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 5.209e-07 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 4.046e-09 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.3103 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.08144 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.06526 Moderately Informative Inherited
Biological Process (BP) cellular biogenic amine metabolic process 0 Informative Direct
Biological Process (BP) positive regulation of transport 0.0005707 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 0.001703 Informative Inherited
Biological Process (BP) polyamine metabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of transmembrane transport 4.352e-07 Highly Informative Direct
Biological Process (BP) regulation of protein catabolic process 0 Highly Informative Direct
Biological Process (BP) cellular biogenic amine biosynthetic process 6.49e-11 Highly Informative Direct
Molecular Function (MF) binding 0.9779 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) isomerase activity 2.55e-05 Moderately Informative Direct
Molecular Function (MF) enzyme regulator activity 2.736e-07 Moderately Informative Direct
Molecular Function (MF) anion binding 0.004596 Moderately Informative Inherited
Molecular Function (MF) enzyme activator activity 5.676e-12 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0 Informative Direct
Molecular Function (MF) racemase and epimerase activity 1.557e-15 Informative Direct
Molecular Function (MF) protein dimerization activity 3.911e-08 Informative Direct
Molecular Function (MF) cofactor binding 4.526e-07 Informative Direct
Molecular Function (MF) carboxy-lyase activity 0 Highly Informative Direct
Molecular Function (MF) pyridoxal phosphate binding 7.154e-12 Highly Informative Direct
Molecular Function (MF) protein homodimerization activity 6.787e-10 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

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)intestine0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)surface structure0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)immune system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)visual system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)skin0InformativeDirect
Xenopus ANatomical entity (XAN)spleen0InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0InformativeDirect
Xenopus ANatomical entity (XAN)tail0InformativeDirect
Xenopus ANatomical entity (XAN)limb0InformativeDirect
Xenopus ANatomical entity (XAN)kidney0InformativeDirect
Xenopus ANatomical entity (XAN)mesonephric kidney0Highly InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Carbon-carbon lyases0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0InformativeDirect
Enzyme Commission (EC)Racemases and epimerases0InformativeDirect
Enzyme Commission (EC)Acting on amino acids and derivatives0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0.02414Moderately InformativeInherited
Biological processLysine biosynthesis0Highly InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationDecarboxylase0InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0Least InformativeDirect
UniPathway (UP)amine and polyamine metabolism5.621e-05Moderately InformativeDirect
UniPathway (UP)nonprotein amino-acid biosynthesis0InformativeDirect
UniPathway (UP)putrescine metabolism0InformativeDirect
UniPathway (UP)alanine metabolism0InformativeDirect
UniPathway (UP)D-alanine biosynthesis0Highly InformativeDirect
UniPathway (UP)putrescine biosynthesis via L-ornithine pathway0Highly InformativeDirect

Document: UP 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) · Disease Ontology (DO) · Xenopus Anatomy (XA) · 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 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) · Disease Ontology (DO) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]