BHCD_PARDP
ID BHCD_PARDP Reviewed; 320 AA.
AC A1B8Z0;
DT 26-FEB-2020, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 1.
DT 03-AUG-2022, entry version 89.
DE RecName: Full=Iminosuccinate reductase {ECO:0000303|PubMed:31723261};
DE EC=1.4.1.- {ECO:0000269|PubMed:31723261};
GN Name=bhcD {ECO:0000303|PubMed:31723261};
GN OrderedLocusNames=Pden_3918 {ECO:0000312|EMBL:ABL71984.1};
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:6RQA}
RP X-RAY CRYSTALLOGRAPHY (2.56 ANGSTROMS) IN COMPLEX WITH NAD, FUNCTION,
RP CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, DISRUPTION PHENOTYPE,
RP 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: Imine reductase that catalyzes the NADH-dependent reduction
CC of iminosuccinate to L-aspartate. Is essential for the growth of
CC P.denitrificans in the presence of glycolate and glyoxylate since it
CC functions in glyoxylate assimilation via the beta-hydroxyaspartate
CC cycle (BHAC). Thereby BhcD regenerates the amino group donor for the
CC first step of the BHAC. {ECO:0000269|PubMed:31723261}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-aspartate + NAD(+) = H(+) + iminosuccinate + NADH;
CC Xref=Rhea:RHEA:42440, ChEBI:CHEBI:15378, ChEBI:CHEBI:29991,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57945, ChEBI:CHEBI:77875;
CC Evidence={ECO:0000269|PubMed:31723261};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:42442;
CC Evidence={ECO:0000269|PubMed:31723261};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.09 mM for iminosuccinate {ECO:0000269|PubMed:31723261};
CC KM=0.02 mM for NADH {ECO:0000269|PubMed:31723261};
CC KM=0.33 mM for NADPH {ECO:0000269|PubMed:31723261};
CC Note=kcat is 201 sec(-1). {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: Iminosuccinate is a labile compound that spontaneously
CC decays into free ammonia and oxaloacetate in solution.
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 ornithine cyclodeaminase/mu-crystallin
CC family. BhcD subfamily. {ECO:0000305|PubMed:31723261}.
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DR EMBL; CP000490; ABL71984.1; -; Genomic_DNA.
DR RefSeq; WP_011750151.1; NC_008687.1.
DR PDB; 6RQA; X-ray; 2.56 A; A/B=1-320.
DR PDBsum; 6RQA; -.
DR AlphaFoldDB; A1B8Z0; -.
DR SMR; A1B8Z0; -.
DR STRING; 318586.Pden_3918; -.
DR PRIDE; A1B8Z0; -.
DR EnsemblBacteria; ABL71984; ABL71984; Pden_3918.
DR KEGG; pde:Pden_3918; -.
DR eggNOG; COG2423; Bacteria.
DR HOGENOM; CLU_042088_2_0_5; -.
DR OMA; HIKGGYV; -.
DR Proteomes; UP000000361; Chromosome 2.
DR GO; GO:0070404; F:NADH binding; IDA:UniProtKB.
DR GO; GO:0016639; F:oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor; IDA:UniProtKB.
DR GO; GO:0046296; P:glycolate catabolic process; IMP:UniProtKB.
DR GO; GO:0009436; P:glyoxylate catabolic process; IMP:UniProtKB.
DR Gene3D; 3.30.1780.10; -; 1.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR003462; ODC_Mu_crystall.
DR InterPro; IPR023401; ODC_N.
DR PANTHER; PTHR13812; PTHR13812; 1.
DR Pfam; PF02423; OCD_Mu_crystall; 1.
DR PIRSF; PIRSF001439; CryM; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
PE 1: Evidence at protein level;
KW 3D-structure; NAD; Nucleotide-binding; Oxidoreductase; Reference proteome.
FT CHAIN 1..320
FT /note="Iminosuccinate reductase"
FT /id="PRO_0000449099"
FT ACT_SITE 67
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:O28608"
FT BINDING 110
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:31723261"
FT BINDING 137..138
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:31723261"
FT BINDING 159
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:31723261"
FT BINDING 199
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:31723261"
FT BINDING 219..222
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:31723261"
FT BINDING 226
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:31723261"
FT BINDING 291
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:31723261"
FT STRAND 1..4
FT /evidence="ECO:0007829|PDB:6RQA"
FT HELIX 6..8
FT /evidence="ECO:0007829|PDB:6RQA"
FT HELIX 9..12
FT /evidence="ECO:0007829|PDB:6RQA"
FT HELIX 15..30
FT /evidence="ECO:0007829|PDB:6RQA"
FT STRAND 33..36
FT /evidence="ECO:0007829|PDB:6RQA"
FT STRAND 40..43
FT /evidence="ECO:0007829|PDB:6RQA"
FT STRAND 50..58
FT /evidence="ECO:0007829|PDB:6RQA"
FT TURN 59..62
FT /evidence="ECO:0007829|PDB:6RQA"
FT STRAND 63..71
FT /evidence="ECO:0007829|PDB:6RQA"
FT HELIX 75..78
FT /evidence="ECO:0007829|PDB:6RQA"
FT STRAND 82..90
FT /evidence="ECO:0007829|PDB:6RQA"
FT TURN 92..94
FT /evidence="ECO:0007829|PDB:6RQA"
FT STRAND 97..102
FT /evidence="ECO:0007829|PDB:6RQA"
FT HELIX 104..122
FT /evidence="ECO:0007829|PDB:6RQA"
FT STRAND 129..133
FT /evidence="ECO:0007829|PDB:6RQA"
FT HELIX 137..149
FT /evidence="ECO:0007829|PDB:6RQA"
FT STRAND 153..158
FT /evidence="ECO:0007829|PDB:6RQA"
FT HELIX 162..164
FT /evidence="ECO:0007829|PDB:6RQA"
FT HELIX 165..174
FT /evidence="ECO:0007829|PDB:6RQA"
FT STRAND 179..181
FT /evidence="ECO:0007829|PDB:6RQA"
FT HELIX 184..190
FT /evidence="ECO:0007829|PDB:6RQA"
FT STRAND 192..196
FT /evidence="ECO:0007829|PDB:6RQA"
FT STRAND 201..205
FT /evidence="ECO:0007829|PDB:6RQA"
FT TURN 207..209
FT /evidence="ECO:0007829|PDB:6RQA"
FT STRAND 212..218
FT /evidence="ECO:0007829|PDB:6RQA"
FT STRAND 227..229
FT /evidence="ECO:0007829|PDB:6RQA"
FT HELIX 231..235
FT /evidence="ECO:0007829|PDB:6RQA"
FT STRAND 237..242
FT /evidence="ECO:0007829|PDB:6RQA"
FT HELIX 244..249
FT /evidence="ECO:0007829|PDB:6RQA"
FT HELIX 254..258
FT /evidence="ECO:0007829|PDB:6RQA"
FT HELIX 264..266
FT /evidence="ECO:0007829|PDB:6RQA"
FT STRAND 267..269
FT /evidence="ECO:0007829|PDB:6RQA"
FT HELIX 270..274
FT /evidence="ECO:0007829|PDB:6RQA"
FT STRAND 285..290
FT /evidence="ECO:0007829|PDB:6RQA"
FT HELIX 295..312
FT /evidence="ECO:0007829|PDB:6RQA"
FT STRAND 316..318
FT /evidence="ECO:0007829|PDB:6RQA"
SQ SEQUENCE 320 AA; 33655 MW; 4CD6659C20328BAD CRC64;
MLVVAEKEIA GLMTPEAAFE AIEAVFASMA RRKAYNFPVV REAIGHEDAL YGFKGGFDAS
ALVLGLKAGG YWPNNQKHNL INHQSTVFLF DPDTGRVSAA VGGNLLTALR TAAASAVSIK
YLAPKGAKVL GMIGAGHQSA FQMRAAANVH RFEKVIGWNP HPEMLSRLAD TAAELGLPFE
AVELDRLGAE ADVIVSITSS FSPLLMNEHV KGPTHIAAMG TDTKGKQELD PALVARARIF
TDEVAQSVSI GECQHAIAAG LIREDQVGEL GAVVAGDDPG RGDAEVTIFD GTGVGLQDLA
VAQAVVELAK HKGVAQEVEI
