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(-) Description

Title :  CRYSTAL STRUCTURE OF RAT BILIVERDIN REDUCTASE AT 1.4 A
 
Authors :  A. Kikuchi, S. Y. Park, Y. Shiro
Date :  08 Aug 00  (Deposition) - 08 Feb 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Biliverdin, Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kikuchi, S. Y. Park, H. Miyatake, D. Sun, M. Sato, T. Yoshida, Y. Shiro
Crystal Structure Of Rat Biliverdin Reductase.
Nat. Struct. Biol. V. 8 221 2001
PubMed-ID: 11224565  |  Reference-DOI: 10.1038/84955
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BILIVERDIN REDUCTASE A
    Chains: A
    EC Number: 1.3.1.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1GCU)

(-) Sites  (0, 0)

(no "Site" information available for 1GCU)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GCU)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:97 -Pro A:98

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GCU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1GCU)

(-) Exons   (0, 0)

(no "Exon" information available for 1GCU)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:292
 aligned with BIEA_RAT | P46844 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:292
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290  
             BIEA_RAT     1 MDAEPKRKFGVVVVGVGRAGSVRLRDLKDPRSAAFLNLIGFVSRRELGSLDEVRQISLEDALRSQEIDVAYICSESSSHEDYIRQFLQAGKHVLVEYPMTLSFAAAQELWELAAQKGRVLHEEHVELLMEEFEFLRREVLGKELLKGSLRFTASPLEEERFGFPAFSGISRLTWLVSLFGELSLISATLEERKEDQYMKMTVQLETQNKGLLSWIEEKGPGLKRNRYVNFQFTSGSLEEVPSVGVNKNIFLKDQDIFVQKLLDQVSAEDLAAEKKRIMHCLGLASDIQKLCH 292
               SCOP domains d1gcua1 A:1-128,A:247-292 Biliverdin reductase                                                                                  d1gcua2 A:129-246 Biliverdin reductase                                                                                d1gcua1 A:1-128,A:247-292 Biliverdin reductase SCOP domains
               CATH domains 1gcuA01 A:1-123,A:245-265 NAD(P)-binding Rossmann-like Domain                                                              1gcuA02 A:124-244,A:266-292 Dihydrodipicolinate Reductase; domain 2                                                      1gcuA01              1gcuA02 A:124-244,A:266-292 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee..hhhhhhhhhhhhhhhhhh.eeeeeee......ee..ee..hhhhhhhh....eeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhh...eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeehhhheeeeeeeee.....eeeeeeee......eeeeeeee..eee..........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gcu A   1 MDAEPKRKFGVVVVGVGRAGSVRLRDLKDPRSAAFLNLIGFVSRRELGSLDEVRQISLEDALRSQEIDVAYICSESSSHEDYIRQFLQAGKHVLVEYPMTLSFAAAQELWELAAQKGRVLHEEHVELLMEEFEFLRREVLGKELLKGSLRFTASPLEEERFGFPAFSGISRLTWLVSLFGELSLISATLEERKEDQYMKMTVQLETQNKGLLSWIEEKGPGLKRNRYVNFQFTSGSLEEVPSVGVNKNIFLKDQDIFVQKLLDQVSAEDLAAEKKRIMHCLGLASDIQKLCH 292
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GCU)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BIEA_RAT | P46844)
molecular function
    GO:0004074    biliverdin reductase activity    Catalysis of the reaction: bilirubin + NAD(P)+ = biliverdin + NAD(P)H + H+.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0042167    heme catabolic process    The chemical reactions and pathways resulting in the breakdown of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  Cis Peptide Bonds
    Tyr A:97 - Pro A:98   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        BIEA_RAT | P46844: 1lc0 1lc3

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