Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V).

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2499879751  61 LYMDVQATTPLDPRVLDAMLPYLVNYYGNPHSRTHAYGWESEAAMERARQ 110
Cdd:PLN02651    1 LYLDMQATTPIDPRVLDAMLPFLIEHFGNPHSRTHLYGWESEDAVEKARA 50

cysteine desulfurase

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2499879751  61 LYMDVQATTPLDPRVLDAMLPYLVNYYGNPHSRTHAYGWESEAAMERARQ 110
Cdd:PLN02651    1 LYLDMQATTPIDPRVLDAMLPFLIEHFGNPHSRTHLYGWESEDAVEKARA 50

Cysteine desulfurase/Cysteine sulfinate desulfinase IscS or related enzyme, NifS family [Amino acid transport and metabolism];

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2499879751  59 RPLYMDVQATTPLDPRVLDAMLPYLVNYYGNPHSrTHAYGWESEAAMERARQ 110
Cdd:COG1104     2 MMIYLDNAATTPVDPEVLEAMLPYLTEYFGNPSS-LHSFGREARAALEEARE 52

cysteine desulfurase

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2499879751  61 LYMDVQATTPLDPRVLDAMLPYLVNYYGNPHSRTHAYGWESEAAMERARQ 110
Cdd:PLN02651    1 LYLDMQATTPIDPRVLDAMLPFLIEHFGNPHSRTHLYGWESEDAVEKARA 50

cysteine desulfurase IscS; This model represents IscS, one of several cysteine desulfurases from a larger protein family designated (misleadingly, in this case) class V aminotransferases. IscS is one of at least 6 enzymes characteristic of the IscSUA-hscAB-fsx system of iron-sulfur cluster assembly. Scoring almost as well as proteobacterial sequences included in the model are mitochondrial cysteine desulfurases, apparently from an analogous system in eukaryotes. The sulfur, taken from cysteine, may be used in other systems as well, such as tRNA base modification and biosynthesis of other cofactors. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Protein synthesis, tRNA and rRNA base modification]

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2499879751  60 PLYMDVQATTPLDPRVLDAMLPYLVNYYGNPHSRTHAYGWESEAAMERARQ 110
Cdd:TIGR02006   4 PIYLDYAATTPVDPRVAEKMMPYLTEKFGNPASRSHSFGWEAEEAVENARN 54

cysteine desulfurase NifS; Members of this protein family are NifS, one of several related families of cysteine desulfurase involved in iron-sulfur (FeS) cluster biosynthesis. NifS is part of the NIF system, usually associated with other nif genes involved in nitrogenase expression and nitrogen fixation. The protein family is given a fairly broad interpretation here. It includes a clade nearly always found in extended nitrogen fixation genomic regions, plus a second clade more closely related to the first than to IscS and also part of NifS-like/NifU-like systems. This model does not extend to a more distantly clade found in the epsilon proteobacteria such as Helicobacter pylori, also named NifS in the literature, built instead in TIGR03403.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2499879751  62 YMDVQATTPLDPRVLDAMLPYLVNYYGNPhSRTHAYGWESEAAMERARQ 110
Cdd:TIGR03402   2 YLDNNATTRVDPEVLEAMLPYFTEYFGNP-SSMHSFGGEVGKAVEEARE 49

Selenocysteine lyase/Cysteine desulfurase [Amino acid transport and metabolism];

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2499879751  62 YMDVQATTPLdPR-VLDAMLPYLVNYYGNPHSRTHAYGWESEAAMERARQ 110
Cdd:COG0520    18 YLDNAATGQK-PRpVIDAIRDYYEPYNANVHRGAHELSAEATDAYEAARE 66