DB code: D00027

CATH domain 3.40.50.720 : Rossmann fold Catalytic domain
3.30.360.10 : Dihydrodipicolinate Reductase; domain 2
E.C. 1.3.1.24
CSA 1gcu
M-CSA 1gcu
MACiE

CATH domain Related DB codes (homologues)
3.40.50.720 : Rossmann fold S00543 S00551 S00552 S00553 S00602 S00604 S00605 S00608 S00610 S00625 S00319 S00328 S00329 S00330 S00331 S00332 D00456 D00457 D00458 S00324 S00320 S00325 S00326 S00327 D00459 S00335 S00336 S00334 T00219 S00339 D00513 D00001 D00002 D00003 D00005 D00007 D00008 D00010 D00012 D00017 D00018 D00023 D00028 D00031 D00032 D00033 D00034 D00035 D00037 D00048 D00071 D00476 D00481 D00482 D00490 D00492 D00494 D00545 D00601 D00603 D00604 D00605 D00615 D00845 D00857 D00858 M00161 M00171 M00210 T00002 T00010 T00011 T00015 T00227 T00247 T00408 T00414 D00827 D00262 D00274 D00275 M00035 T00109
3.30.360.10 : Dihydrodipicolinate Reductase; domain 2 T00219 D00003 D00010 D00017 D00023 D00028 D00034 D00476

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P46844 Biliverdin reductase A
BVR A
EC 1.3.1.24
Biliverdin-IX alpha-reductase
NP_446302.1 (Protein)
NM_053850.1 (DNA/RNA sequence)
PF09166 (Biliv-reduc_cat)
PF01408 (GFO_IDH_MocA)
[Graphical View]

KEGG enzyme name
biliverdin reductase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P46844 BIEA_RAT Bilirubin + NAD(P)(+) = biliverdin + NAD(P)H. Monomer (By similarity). Cytoplasm. Binds 1 zinc ion per subunit.

KEGG Pathways
Map code Pathways E.C.
MAP00860 Porphyrin and chlorophyll metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00038 C00486 C00003 C00006 C00500 C00004 C00005 C00080
E.C.
Compound Zinc Bilirubin NAD+ NADP+ Biliverdin NADH NADPH H+
Type heavy metal amide group,aromatic ring (with nitrogen atoms),carboxyl group amide group,amine group,nucleotide amide group,amine group,nucleotide amide group,aromatic ring (with nitrogen atoms),carboxyl group amide group,amine group,nucleotide amide group,amine group,nucleotide others
ChEBI 29105
16990
15846
18009
17033
16908
16474
15378
PubChem 32051
5280352
5893
5886
439153
5884
1038
1gcuA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1lc0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1lc3A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:NAD Unbound Unbound Unbound
1gcuA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1lc0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1lc3A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot & literature [5] & [8]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1gcuA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 97
1lc0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 97
1lc3A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 97
1gcuA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 279;CYS 280;CYS 291;HIS 292(Zinc binding)
1lc0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 279;CYS 280;CYS 291; (Zinc binding) invisible H292-
1lc3A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 279;CYS 280;CYS 291;HIS 292(Zinc binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[5]
p.224
[6]
p.217
[7]
Fig.4
[8]
Fig.8

References
[1]
Resource AIST-OJ
Comments
Medline ID
PubMed ID 8253726
Journal J Biol Chem
Year 1993
Volume 268
Pages 26099-106
Authors Terry MJ, Maines MD, Lagarias JC
Title Inactivation of phytochrome- and phycobiliprotein-chromophore precursors by rat liver biliverdin reductase.
Related PDB
Related UniProtKB
[2]
Resource
Comments MUTAGENESIS
Medline ID 94291657
PubMed ID 8020496
Journal Eur J Biochem
Year 1994
Volume 222
Pages 597-603
Authors McCoubrey WK Jr, Maines MD
Title Site-directed mutagenesis of cysteine residues in biliverdin reductase. Roles in substrate and cofactor binding.
Related PDB
Related UniProtKB P46844
[3]
Resource
Comments
Medline ID
PubMed ID 9359830
Journal Biochem J
Year 1997
Volume 328
Pages 33-6
Authors Ennis O, Maytum R, Mantle TJ
Title Cloning and overexpression of rat kidney biliverdin IX alpha reductase as a fusion protein with glutathione S-transferase: stereochemistry of NADH oxidation and evidence that the presence of the glutathione S-transferase domain does not effect BVR-A activity.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10957639
Journal Acta Crystallogr D Biol Crystallogr
Year 2000
Volume 56
Pages 1180-2
Authors Sun D, Sato M, Yoshida T, Shimizu H, Miyatake H, Adachi S, Shiro Y, Kikuchi A
Title Crystallization and preliminary X-ray diffraction analysis of a rat biliverdin reductase.
Related PDB 1gcu
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 11224565
Journal Nat Struct Biol
Year 2001
Volume 8
Pages 221-5
Authors Kikuchi A, Park SY, Miyatake H, Sun D, Sato M, Yoshida T, Shiro Y
Title Crystal structure of rat biliverdin reductase.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 11224564
Journal Nat Struct Biol
Year 2001
Volume 8
Pages 215-20
Authors Pereira PJ, Macedo-Ribeiro S, Parraga A, Perez-Luque R, Cunningham O, Darcy K, Mantle TJ, Coll M
Title Structure of human biliverdin IXbeta reductase, an early fetal bilirubin IXbeta producing enzyme.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 11224558
Journal Nat Struct Biol
Year 2001
Volume 8
Pages 198-200
Authors McDonagh AF
Title Turning green to gold.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 12079357
Journal J Mol Biol
Year 2002
Volume 319
Pages 1199-210
Authors Whitby FG, Phillips JD, Hill CP, McCoubrey W, Maines MD
Title Crystal structure of a biliverdin IXalpha reductase enzyme-cofactor complex.
Related PDB 1lc0 1lc3
Related UniProtKB

Comments

Created Updated
2004-03-16 2009-02-26