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(-) Description

Title :  CRYSTAL STRUCTURE OF OXIDATION INTERMEDIATE (1MIN) OF NADH-CYTOCHROME B5 REDUCTASE FROM PIG LIVER
 
Authors :  M. Yamada, T. Tamada, F. Matsumoto, Y. Shoyama, S. Kimura, R. Kuroki, K.
Date :  28 Nov 12  (Deposition) - 17 Jul 13  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Reductase, Cytochrome B5, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Yamada, T. Tamada, K. Takeda, F. Matsumoto, H. Ohno, M. Kosugi, K. Takaba, Y. Shoyama, S. Kimura, R. Kuroki, K. Miki
Elucidations Of The Catalytic Cycle Of Nadh-Cytochrome B5 Reductase By X-Ray Crystallography: New Insights Into Regulation Of Efficient Electron Transfer
J. Mol. Biol. V. 425 4295 2013
PubMed-ID: 23831226  |  Reference-DOI: 10.1016/J.JMB.2013.06.010

(-) Compounds

Molecule 1 - NADH-CYTOCHROME B5 REDUCTASE 3
    Chains: A
    EC Number: 1.6.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CYB5R3, DIA1
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: B5R, CYTOCHROME B5 REDUCTASE, DIAPHORASE-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:63 , PRO A:64 , TYR A:65 , THR A:66 , VAL A:80 , ILE A:81 , LYS A:82 , TYR A:84 , PHE A:85 , PHE A:92 , GLY A:95 , GLY A:96 , LYS A:97 , MET A:98 , SER A:99 , THR A:153 , THR A:156 , NAD A:302 , HOH A:401 , HOH A:402 , HOH A:405 , HOH A:408 , HOH A:409 , HOH A:420 , HOH A:454 , HOH A:557 , HOH A:592 , HOH A:604 , HOH A:630 , HOH A:651 , HOH A:656 , HOH A:681BINDING SITE FOR RESIDUE FAD A 301
2AC2SOFTWARELYS A:82 , TYR A:84 , GLY A:152 , THR A:153 , GLY A:154 , ALA A:180 , ASN A:181 , GLN A:182 , ASP A:211 , PHE A:223 , CYS A:245 , GLY A:246 , PRO A:247 , PRO A:248 , PRO A:249 , MET A:250 , PHE A:272 , FAD A:301 , HOH A:408 , HOH A:410 , HOH A:421 , HOH A:425 , HOH A:432 , HOH A:509 , HOH A:627 , HOH A:631 , HOH A:648 , HOH A:670 , HOH A:679BINDING SITE FOR RESIDUE NAD A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W2H)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:115 -Pro A:116

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W2H)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAD_FRPS51384 Ferredoxin reductase-type FAD binding domain profile.NB5R3_PIG11-123  1A:11-123

(-) Exons   (0, 0)

(no "Exon" information available for 3W2H)

(-) 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:271
 aligned with NB5R3_PIG | P83686 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:271
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271 
            NB5R3_PIG     2 TPAITLENPDIKYPLRLIDKEVVNHDTRRFRFALPSPEHILGLPVGQHIYLSARIDGNLVIRPYTPVSSDDDKGFVDLVIKVYFKDTHPKFPAGGKMSQYLESMKIGDTIEFRGPNGLLVYQGKGKFAIRPDKKSSPVIKTVKSVGMIAGGTGITPMLQVIRAIMKDPDDHTVCHLLFANQTEKDILLRPELEELRNEHSARFKLWYTVDRAPEAWDYSQGFVNEEMIRDHLPPPEEEPLVLMCGPPPMIQYACLPNLERVGHPKERCFAF 272
               SCOP domains d3w2ha1 A:2-125 cytochrome b5 reductase                                                                                     d3w2ha2 A:126-272 cytochrome b5 reductase                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeee....eeeeeee..............eeeeeeee..eeeeeee..........eeeeeee.............hhhhhhhhhh....eeeeeeee..eeeee..eeee........eeee..eeeeeee..hhhhhhhhhhhhhhh.....eeeeeeee.hhhhh.hhhhhhhhhhhh...eeeeeee.........ee...hhhhhhhhh.hhhhh.eeeee.hhhhhhhhhhhhhhhhh.hhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------FAD_FR  PDB: A:11-123 UniProt: 11-123                                                                            ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w2h A   2 TPAITLENPDIKYPLRLIDKEVVNHDTRRFRFALPSPEHILGLPVGQHIYLSARIDGNLVIRPYTPVSSDDDKGFVDLVIKVYFKDTHPKFPAGGKMSQYLESMKIGDTIEFRGPNGLLVYQGKGKFAIRPDKKSSPVIKTVKSVGMIAGGTGITPMLQVIRAIMKDPDDHTVCHLLFANQTEKDILLRPELEELRNEHSARFKLWYTVDRAPEAWDYSQGFVNEEMIRDHLPPPEEEPLVLMCGPPPMIQYACLPNLERVGHPKERCFAF 272
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271
   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: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W2H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W2H)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NB5R3_PIG | P83686)
molecular function
    GO:0004128    cytochrome-b5 reductase activity, acting on NAD(P)H    Catalysis of the reaction: NAD(P)H + H+ + 2 ferricytochrome b(5) = NAD(P)+ + 2 ferrocytochrome b(5).
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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.
biological process
    GO:0006695    cholesterol biosynthetic process    The chemical reactions and pathways resulting in the formation of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
    GO:0008203    cholesterol metabolic process    The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    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.
    GO:0006694    steroid biosynthetic process    The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    GO:0016126    sterol biosynthetic process    The chemical reactions and pathways resulting in the formation of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NB5R3_PIG | P83686: 1ndh 3w2e 3w2f 3w2g 3w2i 3w5h 5gv7 5gv8

(-) Related Entries Specified in the PDB File

1ndh 3w2e 3w2f 3w2g 3w2i 3w5h