BHCC_PARDP
ID BHCC_PARDP Reviewed; 387 AA.
AC A1B8Z1;
DT 26-FEB-2020, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 1.
DT 03-AUG-2022, entry version 78.
DE RecName: Full=3-hydroxy-D-aspartate aldolase {ECO:0000305|PubMed:31723261};
DE EC=4.1.3.41 {ECO:0000269|PubMed:31723261};
DE AltName: Full=beta-hydroxyaspartate aldolase {ECO:0000303|PubMed:31723261};
GN Name=bhcC {ECO:0000303|PubMed:31723261};
GN OrderedLocusNames=Pden_3919 {ECO:0000312|EMBL:ABL71985.1};
OS Paracoccus denitrificans (strain Pd 1222).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC Rhodobacteraceae; Paracoccus.
OX NCBI_TaxID=318586;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Pd 1222;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA Munk A.C., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Schmutz J.,
RA Larimer F., Land M., Hauser L., Kyrpides N., Lykidis A., Spiro S.,
RA Richardson D.J., Moir J.W.B., Ferguson S.J., van Spanning R.J.M.,
RA Richardson P.;
RT "Complete sequence of chromosome 2 of Paracoccus denitrificans PD1222.";
RL Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0007744|PDB:6QKB}
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEX WITH PLP AND MAGNESIUM,
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
RP SUBUNIT, DISRUPTION PHENOTYPE, AND INDUCTION.
RC STRAIN=ATCC 17741 / DSM 413 / NBRC 16712 / NCCB 22021 / NCIMB 11627;
RX PubMed=31723261; DOI=10.1038/s41586-019-1748-4;
RA Schada von Borzyskowski L., Severi F., Krueger K., Hermann L., Gilardet A.,
RA Sippel F., Pommerenke B., Claus P., Cortina N.S., Glatter T., Zauner S.,
RA Zarzycki J., Fuchs B.M., Bremer E., Maier U.G., Amann R.I., Erb T.J.;
RT "Marine Proteobacteria metabolize glycolate via the beta-hydroxyaspartate
RT cycle.";
RL Nature 575:500-504(2019).
CC -!- FUNCTION: Catalyzes the condensation of glyoxylate and glycine into
CC (2R,3S)-beta-hydroxyaspartate ((3S)-3-hydroxy-D-aspartate). Is
CC essential for the growth of P.denitrificans in the presence of
CC glycolate and glyoxylate since it functions in glyoxylate assimilation
CC via the beta-hydroxyaspartate cycle (BHAC). Is also able to catalyze
CC the reverse reaction in vitro, i.e. the cleavage of (3S)-3-hydroxy-D-
CC aspartate, and that of D-threonine to a lesser extent.
CC {ECO:0000269|PubMed:31723261}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(3S)-3-hydroxy-D-aspartate = glycine + glyoxylate;
CC Xref=Rhea:RHEA:27934, ChEBI:CHEBI:36655, ChEBI:CHEBI:57305,
CC ChEBI:CHEBI:60894; EC=4.1.3.41;
CC Evidence={ECO:0000269|PubMed:31723261};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:27936;
CC Evidence={ECO:0000269|PubMed:31723261};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(3R)-3-hydroxy-D-aspartate = glycine + glyoxylate;
CC Xref=Rhea:RHEA:27938, ChEBI:CHEBI:36655, ChEBI:CHEBI:57305,
CC ChEBI:CHEBI:60898; EC=4.1.3.41;
CC Evidence={ECO:0000250|UniProtKB:Q8GRC8};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:31723261};
CC Note=Binds 1 pyridoxal phosphate per subunit.
CC {ECO:0000269|PubMed:31723261};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:31723261};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.23 mM for glyoxylate {ECO:0000269|PubMed:31723261};
CC KM=4.31 mM for glycine {ECO:0000269|PubMed:31723261};
CC KM=0.28 mM for (3S)-3-hydroxy-D-aspartate
CC {ECO:0000269|PubMed:31723261};
CC KM=9.24 mM for D-threonine {ECO:0000269|PubMed:31723261};
CC Note=kcat is 91 sec(-1) for the condensation of glyoxylate and
CC glycine. kcat is 33 sec(-1) for the cleavage of (3S)-3-hydroxy-D-
CC aspartate. kcat is 76 sec(-1) for the cleavage of D-threonine into
CC acetaldehyde and glycine (PubMed:31723261).
CC {ECO:0000269|PubMed:31723261};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:31723261}.
CC -!- INDUCTION: Induced by glycolate. {ECO:0000269|PubMed:31723261}.
CC -!- DISRUPTION PHENOTYPE: Abolishes growth on glycolate or glyoxylate, but
CC the deletion mutant strain is still able to grow on acetate, succinate
CC or glucose with comparable growth rates as for the wild type.
CC {ECO:0000269|PubMed:31723261}.
CC -!- MISCELLANEOUS: The beta-hydroxyaspartate cycle (BHAC) consists of BhcA,
CC BhcB, BhcC, and BhcD enzyme activities. Overall, it converts two
CC molecules of glyoxylate (C2) into oxaloacetate (C4) without the loss of
CC carbon as CO2, under consumption of just one reducing equivalent and
CC regeneration of the catalytic amino donor, which makes it one of the
CC most efficient glyoxylate assimilation pathways. This cycle is of
CC ecological importance in the assimilation of phytoplankton-derived
CC dissolved organic carbon in marine environments by marine
CC Proteobacteria, and suggests a trophic interaction between autotrophic
CC phytoplankton and heterotrophic bacterioplankton. Oxaloacetate formed
CC in the BHAC can directly enter the tricarboxylic acid cycle or serve as
CC substrate for anabolic reactions. {ECO:0000305|PubMed:31723261}.
CC -!- SIMILARITY: Belongs to the DSD1 family. {ECO:0000305}.
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DR EMBL; CP000490; ABL71985.1; -; Genomic_DNA.
DR RefSeq; WP_011750152.1; NC_008687.1.
DR PDB; 6QKB; X-ray; 1.70 A; A/B=1-387.
DR PDBsum; 6QKB; -.
DR AlphaFoldDB; A1B8Z1; -.
DR SMR; A1B8Z1; -.
DR STRING; 318586.Pden_3919; -.
DR PRIDE; A1B8Z1; -.
DR EnsemblBacteria; ABL71985; ABL71985; Pden_3919.
DR KEGG; pde:Pden_3919; -.
DR eggNOG; COG3616; Bacteria.
DR HOGENOM; CLU_031639_2_0_5; -.
DR OMA; RGGIKDV; -.
DR Proteomes; UP000000361; Chromosome 2.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0016833; F:oxo-acid-lyase activity; IDA:UniProtKB.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IDA:UniProtKB.
DR GO; GO:0046296; P:glycolate catabolic process; IMP:UniProtKB.
DR GO; GO:0009436; P:glyoxylate catabolic process; IMP:UniProtKB.
DR Gene3D; 2.40.37.20; -; 1.
DR Gene3D; 3.20.20.10; -; 1.
DR InterPro; IPR001608; Ala_racemase_N.
DR InterPro; IPR026956; D-ser_dehydrat-like_dom.
DR InterPro; IPR042208; D-ser_dehydrat-like_sf.
DR InterPro; IPR029066; PLP-binding_barrel.
DR Pfam; PF01168; Ala_racemase_N; 1.
DR Pfam; PF14031; D-ser_dehydrat; 1.
DR SMART; SM01119; D-ser_dehydrat; 1.
DR SUPFAM; SSF51419; SSF51419; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Magnesium; Metal-binding; Pyridoxal phosphate;
KW Reference proteome.
FT CHAIN 1..387
FT /note="3-hydroxy-D-aspartate aldolase"
FT /id="PRO_0000449100"
FT BINDING 85
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:31723261"
FT BINDING 238
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:31723261"
FT BINDING 256..257
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:31723261"
FT BINDING 265
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:31723261"
FT BINDING 355
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:31723261"
FT BINDING 357
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:31723261"
FT MOD_RES 62
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000269|PubMed:31723261"
FT HELIX 7..9
FT /evidence="ECO:0007829|PDB:6QKB"
FT TURN 12..14
FT /evidence="ECO:0007829|PDB:6QKB"
FT HELIX 24..26
FT /evidence="ECO:0007829|PDB:6QKB"
FT STRAND 29..35
FT /evidence="ECO:0007829|PDB:6QKB"
FT HELIX 36..52
FT /evidence="ECO:0007829|PDB:6QKB"
FT TURN 61..64
FT /evidence="ECO:0007829|PDB:6QKB"
FT HELIX 67..77
FT /evidence="ECO:0007829|PDB:6QKB"
FT STRAND 82..86
FT /evidence="ECO:0007829|PDB:6QKB"
FT HELIX 87..95
FT /evidence="ECO:0007829|PDB:6QKB"
FT STRAND 99..106
FT /evidence="ECO:0007829|PDB:6QKB"
FT HELIX 110..118
FT /evidence="ECO:0007829|PDB:6QKB"
FT HELIX 119..122
FT /evidence="ECO:0007829|PDB:6QKB"
FT STRAND 125..132
FT /evidence="ECO:0007829|PDB:6QKB"
FT HELIX 135..146
FT /evidence="ECO:0007829|PDB:6QKB"
FT STRAND 150..156
FT /evidence="ECO:0007829|PDB:6QKB"
FT STRAND 162..165
FT /evidence="ECO:0007829|PDB:6QKB"
FT HELIX 168..180
FT /evidence="ECO:0007829|PDB:6QKB"
FT STRAND 184..190
FT /evidence="ECO:0007829|PDB:6QKB"
FT TURN 195..198
FT /evidence="ECO:0007829|PDB:6QKB"
FT HELIX 202..225
FT /evidence="ECO:0007829|PDB:6QKB"
FT STRAND 231..235
FT /evidence="ECO:0007829|PDB:6QKB"
FT TURN 238..240
FT /evidence="ECO:0007829|PDB:6QKB"
FT HELIX 241..244
FT /evidence="ECO:0007829|PDB:6QKB"
FT STRAND 247..249
FT /evidence="ECO:0007829|PDB:6QKB"
FT HELIX 257..259
FT /evidence="ECO:0007829|PDB:6QKB"
FT HELIX 263..266
FT /evidence="ECO:0007829|PDB:6QKB"
FT TURN 276..280
FT /evidence="ECO:0007829|PDB:6QKB"
FT STRAND 285..293
FT /evidence="ECO:0007829|PDB:6QKB"
FT STRAND 299..303
FT /evidence="ECO:0007829|PDB:6QKB"
FT HELIX 306..308
FT /evidence="ECO:0007829|PDB:6QKB"
FT STRAND 325..329
FT /evidence="ECO:0007829|PDB:6QKB"
FT STRAND 334..337
FT /evidence="ECO:0007829|PDB:6QKB"
FT STRAND 348..352
FT /evidence="ECO:0007829|PDB:6QKB"
FT HELIX 356..360
FT /evidence="ECO:0007829|PDB:6QKB"
FT STRAND 364..370
FT /evidence="ECO:0007829|PDB:6QKB"
FT STRAND 373..379
FT /evidence="ECO:0007829|PDB:6QKB"
FT TURN 381..384
FT /evidence="ECO:0007829|PDB:6QKB"
SQ SEQUENCE 387 AA; 41786 MW; 831CE7FF51A8F0CA CRC64;
MNAKTDFSGY EVGYDIPALP GMDESEIQTP CLILDLDALE RNIRKMGDYA KAHGMRHRSH
GKMHKSVDVQ KLQESLGGSV GVCCQKVSEA EAFARGGIKD VLVTNEVREP AKIDRLARLP
KTGATVTVCV DDVQNIADLS AAAQKHGTEL GIFVEIDCGA GRCGVTTKEA VVEIAKAAAA
APNLTFKGIQ AYQGAMQHMD SFEDRKAKLD AAIAQVKEAV DALEAEGLAP EFVSGGGTGS
YYFESNSGIY NELQCGSYAF MDADYGRIHD AEGKRIDQGE WENALFILTS VMSHAKPHLA
VVDAGLKAQS VDSGLPFVYG RDDVKYIKCS DEHGVVEDKD GVLKVNDKLR LVPGHCDPTC
NVHDWYVGVR NGKVETVWPV SARGKGY
