Uncharacterized conserved protein, cupin superfamily [Function unknown];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517053874  10 IVHWSEIERPDDshyddddelMSIGAPFGRYFGLAKLGIHHERLPPGRRTSFPHAESAEEEFVYVLEGEPDVWLDGHLYR 89
Cdd:COG3837    1 IVNLDDLPGPEA---------GRRYRRLGDALGLTRLGVNLITLPPGASSSPYHAHSAEEEFVYVLEGELTLRIGGEEYV 71

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 517053874  90 LKQGDAVGFPAgtGIAHSFLNNTQAEVHLLVVGERHK 126
Cdd:COG3837   72 LEPGDSVGFPA--GVPHRLRNRGDEPARYLVVGTRAP 106

(S)-ureidoglycine aminohydrolase;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 517053874  69 EEFVYVLEGEPDVWLDGHLYRLKQGDAVGFPAGTGiaHSFLNNTQAEVHLLVVGERH 125
Cdd:PRK11171  84 ETFLFVVEGEITLTLEGKTHALSEGGYAYLPPGSD--WTLRNAGAEDARFHWIRKRY 138

Uncharacterized conserved protein, cupin superfamily [Function unknown];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517053874  10 IVHWSEIERPDDshyddddelMSIGAPFGRYFGLAKLGIHHERLPPGRRTSFPHAESAEEEFVYVLEGEPDVWLDGHLYR 89
Cdd:COG3837    1 IVNLDDLPGPEA---------GRRYRRLGDALGLTRLGVNLITLPPGASSSPYHAHSAEEEFVYVLEGELTLRIGGEEYV 71

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 517053874  90 LKQGDAVGFPAgtGIAHSFLNNTQAEVHLLVVGERHK 126
Cdd:COG3837   72 LEPGDSVGFPA--GVPHRLRNRGDEPARYLVVGTRAP 106

XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; This family contains transcriptional regulators containing an N-terminal XRE (Xenobiotic Response Element) family helix-turn-helix (HTH) DNA-binding domain and a C-terminal cupin domain. Included in this family is Escherichia coli transcription factor SutR (YdcN) that plays a regulatory role in sulfur utilization; it regulates a set of genes involved in the generation of sulfate and its reduction, the synthesis of cysteine, the synthesis of enzymes containing Fe-S as cofactors, and the modification of tRNA with use of sulfur-containing substrates. This family belongs to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 517053874  45 KLGIHHERLPPG--RRTSFPHAEsaeEEFVYVLEGEPDVWLDGHLYRLKQGDAVGFPAgtGIAHSFLNNTQAEVHLLVV 121
Cdd:cd02209   15 KMEPFLVTLPPGgsGGEPYSHEG---EEFGYVLEGELELTVGGETYVLEAGDSIYFDS--DVPHRYRNPGDEPARVLWV 88

(S)-ureidoglycine aminohydrolase and related proteins, N-terminal cupin domain; This family includes the N-terminal cupin domain of (S)-ureidoglycine aminohydrolase (UGlyAH), an enzyme that converts (S)-ureidoglycine into (S)-ureidoglycolate and ammonia, providing the final substrate to the ureide pathway. The ureide pathway has recently been identified as the metabolic route of purine catabolism in plants and some bacteria where, uric acid, which is a major product of the early stage of purine catabolism, is degraded into glyoxylate and ammonia via stepwise reactions by seven different enzymes. Thus, this pathway has a possible physiological role in mobilization of purine ring nitrogen for further assimilation. This enzyme from Arabidopsis thaliana(AtUGlyAH) has been shown to bind a Mn2+ ion, via the C-terminal cupin domain, which acts as a molecular anchor to bind (S)-ureidoglycine, and its binding mode dictates the enantioselectivity of the reaction. The structure of AtUGlyAH shows a bi-cupin fold with a conserved "jelly roll-like" beta-barrel fold and an octameric functional unit. Several structural homologs of UGlyAH, including the Escherichia coli ortholog YlbA (also known as GlxB6), also exhibit similar features.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 517053874  53 LPPGRRTSFPHAESAEEEFVYVLEGEPDVWLDGHLYRLKQGDAVGFPAGTGiaHSFLNNTQAEVHLLVV 121
Cdd:cd02211   32 VEPGGGSTAPEGGEGIERFLYVLEGEVELTVGGETHTLTAGGYAYLPPGTK--HSLRNAGDEPARLLWY 98

Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes mostly bacterial proteins homologous to dimethylsulfoniopropionate lyase DddK from marine bacterium Pelagibacter. DddK cleaves dimethylsulfoniopropionate (DMSP), the organic osmolyte and antioxidant produced in marine environments, and yields acrylate and the climate-active gas dimethyl sulfide (DMS). DddK contains a double-stranded beta-helical motif which utilizes various divalent metal ions as cofactors for catalytic activity; however, nickel, an abundant metal ion in marine environments, confers the highest DMSP lyase activity. Also included in this family is Plu4264, a Photorhabdus luminescens manganese-containing cupin shown to have similar metal binding site to TM1287 decarboxylase, but two very different substrate binding pockets. The Plu4264 binding pocket shows a cavity and substrate entry point more than twice as large as and more hydrophobic than TM1287, suggesting that Plu4264 accepts a substrate that is significantly larger than that of TM1287, a putative oxalate decarboxylase. Thus, the function of Plu4264 could be similar to that of TM1287 but with a larger, less charged substrate. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 517053874  59 TSFPHAESaEEEFVYVLEGEPDVWLDGHLYRLKQGDAVGFPAGTgiAHSFLNNTQAEVHLLVV 121
Cdd:cd06988   14 TSTPHSHH-EYEIFIVISGKGIVVVDGEREPVKAGDVVYIPPGT--EHYVKNDGDEDFEFYSI 73

quercetinase, N- and C-terminal cupin domains; This family contains quercetinase (also known as quercetin 2,3-dioxygenase, 2,3QD, QDO and YxaG; EC 1.13.11.24), a mononuclear copper-dependent dioxygenase that catalyzes the cleavage of the flavonol quercetin (5,7,3',4'-tetrahydroxyflavonol) heterocyclic ring to produce 2-protocatechuoyl-phloroglucinol carboxylic acid and carbon monoxide. Bacillus subtilis quercetin 2,3-dioxygenase (QDO) is a homodimer that shows oxygenase activity with several divalent metals such as Mn2+, Co2+, Fe2+, and Cu2+, although the preferred one appears to be Mn2+. The dioxygen binds to the metal ion of the Cu-QDO-quercetin complex, yielding a Cu2+-superoxo quercetin radical intermediate, which then forms a Cu2+-alkylperoxo complex which then evolves into endoperoxide intermediate that decomposes to the product. Quercetinase is a bicupin with two tandem cupin beta-barrel domains, both of which are included in this alignment model. The pirins, which also belong to the cupin domain family, have been shown to catalyze a reaction involving quercetin and may have a function similar to that of quercetinase.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 517053874  62 PHAESAEEEFVYVLEGEPDVWLDGHLYRLKQGDAVGFPAGTgiAHSF 108
Cdd:cd02215   47 PHYHKRHHETFYVLEGRLQLWLDGESRLLTPGDFASVPPGT--IHAY 91

Ureidoglycine aminohydrolase [Nucleotide transport and metabolism];

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 517053874  55 PGRRTSFPHAESAEEEFVYVLEGEPDVWLDGHLYRLKQGDAVGFPAGTGiaHSFLNNTQAEVHLLVVGERHKA 127
Cdd:COG3257   68 PGGGSDRPEPDPGAETFLFVLEGEVTLTLGGETHELTPGGYAYLPPGTP--WTLRNAGDEPARFHWIRKRYEP 138

(S)-ureidoglycine aminohydrolase;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 517053874  69 EEFVYVLEGEPDVWLDGHLYRLKQGDAVGFPAGTGiaHSFLNNTQAEVHLLVVGERH 125
Cdd:PRK11171  84 ETFLFVVEGEITLTLEGKTHALSEGGYAYLPPGSD--WTLRNAGAEDARFHWIRKRY 138

Methanocaldococcus jannaschii MJ1618 and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to MJ1618, a Methanocaldococcus jannaschii protein of unknown function with a cupin beta barrel domain. The active site of members of the cupin superfamily is generally located at the center of a conserved barrel and usually includes a metal ion.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 517053874  50 HERLPPGRRTSfPHAESAEEEFVYVLEGEPDVWLDGHLYRLKQGDAVGFPAGT 102
Cdd:cd02214   23 HARVPPGESTL-PHRLKGSEEVYYILEGEGTMEIDGEPREVGPGDAVLIPPGA 74

Thermotoga maritima TM1112 and related proteins, cupin domain; This family includes bacterial and plant proteins homologous to TM1112, a Thermotoga maritima protein of unknown function with a cupin beta barrel domain. TM1112 (also known as DUF861) is a subfamily of RmlC-like cupins with a conserved "jelly roll-like" beta-barrel fold; structures indicate that a monomer is the biologically-relevant form.

                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 517053874  68 EEEFVYVLEGE----PDvwlDGHLYRLKQGDAVGFPAGT 102
Cdd:cd02227   18 EDEFCYILEGEvrvtPE---DGEPVTFKAGDLVVFPAGF 53

TcmJ monooxygenase and related proteins, cupin domain; This family includes TcmJ, a subunit of the tetracenomycin (TCM) polyketide synthase (PKS) type II complex in Streptomyces glaucescens. TcmJ is a quinone-forming monooxygenase involved in the modification of aromatic polyketides synthesized by polyketide synthases of types II and III. Orthologs of TcmJ include the Streptomyces BenD (benastatin biosynthetic pathway), the Streptomyces olivaceus ElmJ (polyketide antibiotic elloramycin biosynthetic pathway), the Actinomadura hibisca PdmL (pradimicin biosynthetic pathway), the Streptomyces cyaneus CurC (curamycin biosynthetic pathway), the Streptomyces rishiriensis Lct30 (lactonamycin biosynthetic pathway), and the Streptomyces WhiE II (spore pigment polyketide biosynthetic pathway). Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 517053874  50 HERLPPGRRTSfPHAESAEEEFVYVLEGEPDVWLDGHLYRLKQGDAVGFPAGTgiAHSFLNNTQAEVHL 118
Cdd:cd06991   23 TLTLAPGERVS-EHYHPYSEEFLYVVRGRLVVRVDGEPVVLEAGEALLVPRGV--RHRLENAGDEPARL 88

Helicobacter pylori HP0902 and related proteins, cupin domain; This family includes prokaryotic and archaeal proteins homologous to HP0902, a functionally uncharacterized protein from Helicobacter pylori and Spy1581, a protein of unknown function from Streptococcus pyogenes. These proteins demonstrate all-beta cupin folds that cannot bind metal ions due to the absence of a metal-binding histidine that is conserved in many metallo-cupins. HP0902 is able to bind bacterial endotoxin lipopolysaccharides (LPS) through its surface-exposed loops, where metal-binding sites are usually found in other metallo-cupins, and thus may have a putative role in H. pylori pathogenicity.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 517053874  71 FVYVLEGEPDVWLDGHLYRLKQGDAVGFPAgtGIAHSfLNNTQAEVHLLVV 121
Cdd:cd02230   34 TVQVLEGEAEFTIGGETVTLKAGELIVMPA--NVPHA-LKAEEDFKMLLTL 81