HAMAP rule MF_01825
General rule information
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| Accession | MF_01825 |
| Dates | 19-MAR-2004 (Created) 19-NOV-2022 (Last updated, Version 19) |
| Name | PdxB |
| Scope | Bacteria; Bacteroidota
Bacteria; Gammaproteobacteria |
| Templates | P05459 (PDXB_ECOLI); Q9I3W9 (PDXB_PSEAE): [Recover all] |
| Triggered by |
Propagated annotation
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Identifier, protein and gene names
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| Identifier |
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| Protein name |
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| Gene name |
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Comments
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| Function | Catalyzes the oxidation of erythronate-4-phosphate to 3-hydroxy-2-oxo-4-phosphonooxybutanoate. |
| Catalytic activity | RHEA:18829: 4-phospho-D-erythronate + NAD(+) = (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + H(+) + NADH
EC 1.1.1.290 |
| Pathway | Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 2/5. |
| Subunit | Homodimer. |
| Subcellular location | Cytoplasm. |
| Similarity | Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. PdxB subfamily. |
Keywords
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Gene Ontology
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GO:0016491; Molecular function: oxidoreductase activity.
GO:0008615; Biological process: pyridoxine biosynthetic process.
GO:0005737; Cellular component: cytoplasm.
GO:0008615; Biological process: pyridoxine biosynthetic process.
GO:0005737; Cellular component: cytoplasm.
Cross-references
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| PROSITE | PS00065; D_2_HYDROXYACID_DH_1; 1; |
| PS00670; D_2_HYDROXYACID_DH_2; 1; | |
| PS00671; D_2_HYDROXYACID_DH_3; 1; | |
| Pfam | PF00389; 2-Hacid_dh; 1; |
| PF02826; 2-Hacid_dh_C; 1; | |
| PRINTS | PR00411; PNDRDTASEI; 1; |
Features
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| From: PDXB_PSEAE (Q9I3W9) | ||||||||||||
| Key | From | To | Description | Tag | Condition | FTGroup | ||||||
| BINDING (Optional) | 126 | 127 | /ligand="NAD(+)" /ligand_id="ChEBI:CHEBI:57540 | Q-V | ||||||||
| BINDING (Optional) | 206 | 208 | /ligand="NAD(+)" /ligand_id="ChEBI:CHEBI:57540 | A-S-R | ||||||||
| ACT_SITE | 208 | 208 | R | |||||||||
| ACT_SITE | 237 | 237 | E | |||||||||
| ACT_SITE | 254 | 254 | Proton donor | H | ||||||||
| BINDING (Optional) | 45 | 45 | /ligand="substrate | [ST] | ||||||||
| BINDING (Optional) | 66 | 66 | /ligand="substrate | T | ||||||||
| BINDING (Optional) | 146 | 146 | /ligand="NAD(+)" /ligand_id="ChEBI:CHEBI:57540 | D | ||||||||
| BINDING (Optional) | 175 | 175 | /ligand="NAD(+)" /ligand_id="ChEBI:CHEBI:57540 | T | ||||||||
| BINDING (Optional) | 232 | 232 | /ligand="NAD(+)" /ligand_id="ChEBI:CHEBI:57540 | D | ||||||||
| BINDING (Optional) | 257 | 257 | /ligand="NAD(+)" /ligand_id="ChEBI:CHEBI:57540 | G | ||||||||
| BINDING (Optional) | 258 | 258 | /ligand="substrate | Y | ||||||||
Additional information
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| Size range | 345-393 amino acids |
| Related rules | None |
| Fusion | None |
| Comments | The pyridoxal phosphate can be synthetised from two separate branches: the pdxA branch (that requires the gapA (or epd), pdxB, serC and pdxA enzymes) and the pdxJ branch (that requires the dxs and pdxJ enzymes) that start different precursors. Both branches for the last step (pdxH) of the from pyridoxal phosphate pathway. |