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(-) Description

Title :  CRYSTAL STRUCTURE OF A BILIVERDIN REDUCTASE ENZYME-COFACTOR COMPLEX
 
Authors :  F. G. Whitby, J. D. Phillips, C. P. Hill, W. Mccoubrey, M. D. Maines
Date :  05 Apr 02  (Deposition) - 17 Jul 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Biliverdin Reductase, Tetrapyrrole, Bile Pigment, Bilirubin, Heme, Nadh, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. G. Whitby, J. D. Phillips, C. P. Hill, W. Mccoubrey, M. D. Maines
Crystal Structure Of A Biliverdin Ixalpha Reductase Enzyme-Cofactor Complex.
J. Mol. Biol. V. 319 1199 2002
PubMed-ID: 12079357  |  Reference-DOI: 10.1016/S0022-2836(02)00383-2
(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
    Synonym: BILIVERDIN-IX ALPHA-REDUCTASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2PO43Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:15 , VAL A:16 , SER A:43 , ARG A:44 , ARG A:45 , LYS A:209 , HOH A:1095BINDING SITE FOR RESIDUE PO4 A 601
2AC2SOFTWARESER A:102 , PHE A:103 , ALA A:104 , SER A:285 , LYS A:289 , NAD A:901 , HOH A:1023 , HOH A:1075BINDING SITE FOR RESIDUE PO4 A 602
3AC3SOFTWAREPHE A:151 , ARG A:171 , ARG A:224 , NAD A:900BINDING SITE FOR RESIDUE PO4 A 604
4AC4SOFTWAREARG A:18 , ALA A:19 , SER A:74 , SER A:76 , HIS A:79 , GLU A:96 , TYR A:97 , PRO A:98 , GLU A:123 , LEU A:156 , PHE A:161 , SER A:167 , PO4 A:604 , HOH A:1005 , HOH A:1025 , HOH A:1107 , HOH A:1150 , HOH A:1218BINDING SITE FOR RESIDUE NAD A 900
5AC5SOFTWAREMET A:2 , ILE A:3 , GLU A:66 , PHE A:103 , GLN A:107 , LYS A:223 , VAL A:245 , GLN A:264 , LYS A:289 , GLN A:293 , PO4 A:602 , HOH A:1052 , HOH A:1091 , HOH A:1178BINDING SITE FOR RESIDUE NAD A 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LC3)

(-) 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 1LC3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1LC3)

(-) Exons   (0, 0)

(no "Exon" information available for 1LC3)

(-) 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:293
                                    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 MDAEPKRKFGVVVVGVGRAGSVRLRDLKDPRSAAFLNLIGFVSRRELGSLDEVRQISLEDALRSQEIDVAYICSESSSHEDYIRQFLQAGKHVLVEYPMTLSFAAAQELWELAAQKGRVLHEEHVELLMEEFEFLRREVLGKELLKGSLRFTASPLEEERFGFPAFSGISRLTWLVSLFGELSLISATLEERKEDQYMKMTVQLETQNKGLLSWIEEKGPGLKRNRYVNFQFTSGSLEEVPSVGVNKNIFLKDQDIFVQKLLDQVSAEDLAAEKKRIMHCLGLASDIQKLCHQ 293
               SCOP domains d1lc3 a1 A:2-128,A:247-293 Biliverdin reductase                                                                                 d1lc3a2 A:129-246 Biliverdin reductase                                                                                d1lc3a1 A:2-128,A:247-293 Biliverdin reductase  SCOP domains
               CATH domains 1lc3A 01 A:2-123,A:245-265 NAD(P)-binding Rossmann-like Domain                                                             1lc3A02 A:124-244,A:266-292 Dihydrodipicolinate Reductase; domain 2                                                      1lc3A01              1lc3A02 A:124-244,A:266-292- CATH domains
               Pfam domains --------GFO_IDH_MocA-1lc3A01 A:9-124                                                                                        ------Biliv-reduc_cat-1lc3A02 A:131-245                                                                                  ------------------------------------------------ Pfam domains
         Sec.struct. author .....-..eeeeee..hhhhhhhhhhhhhhhhhh.eeeeeee......ee..ee..hhhhhhhh....eeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhh...eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeehhhheeeeeeeee.....eeeeeeee......eeeeeeee...ee..........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lc3 A   2 MITNS-GKFGVVVVGVGRAGSVRLRDLKDPRSAAFLNLIGFVSRRELGSLDEVRQISLEDALRSQEIDVAYICSESSSHEDYIRQFLQAGKHVLVEYPMTLSFAAAQELWELAAQKGRVLHEEHVELLMEEFEFLRREVLGKELLKGSLRFTASPLEEERFGFPAFSGISRLTWLVSLFGELSLISATLEERKEDQYMKMTVQLETQNKGLLSWIEEKGPGLKRNRYVNFQFTSGSLEEVPSVGVNKNIFLKDQDIFVQKLLDQVSAEDLAAEKKRIMHCLGLASDIQKLCHQ 293
                                | | 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   
                                6 7
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: Biliv-reduc_cat] (2)

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        BIEA_RAT | P46844: 1gcu 1lc0

(-) Related Entries Specified in the PDB File

1lc0 STRUCTURE OF BILIVERDIN REDUCTASE AND THE ENZYME-NADH COMPLEX