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(-) Description

Title :  THE STRUCTURE OF PHYSARUM POLYCEPHALUM CYTOCHROME B5 REDUCTASE
 
Authors :  S. W. Kim, M. Suga, K. Ogasahara, T. Ikegami, Y. Minami, T. Yubisui, T. Ts
Date :  14 Mar 07  (Deposition) - 17 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.56
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Flavoprotein, Fad-Binding Domain, Nadh-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kim, M. Suga, K. Ogasahara, T. Ikegami, Y. Minami, T. Yubisui, T. Tsukihara
Structure Of Physarum Polycephalum Cytochrome B5 Reductase At 1. 56 A Resolution.
Acta Crystallogr. , Sect. F V. 63 274 2007
PubMed-ID: 17401193  |  Reference-DOI: 10.1107/S1744309107010731

(-) Compounds

Molecule 1 - NADH-CYTOCHROME B5 REDUCTASE
    Chains: A, B
    EC Number: 1.6.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC13
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 39-281
    Organism Scientific: PHYSARUM POLYCEPHALUM
    Organism Taxid: 5791

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL2Ligand/IonGLYCEROL
3IOD4Ligand/IonIODIDE ION
4NA2Ligand/IonSODIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:181 , LEU A:200BINDING SITE FOR RESIDUE IOD A 1502
2AC2SOFTWARESER A:87BINDING SITE FOR RESIDUE IOD A 1503
3AC3SOFTWARESER B:87 , ARG B:99 , HOH B:1694BINDING SITE FOR RESIDUE IOD B 1504
4AC4SOFTWARENA A:1602 , MET B:259BINDING SITE FOR RESIDUE NA B 1601
5AC5SOFTWAREMET A:259 , NA B:1601BINDING SITE FOR RESIDUE NA A 1602
6AC6SOFTWAREARG A:99 , PRO A:100 , TYR A:101 , THR A:102 , ILE A:116 , ILE A:117 , LYS A:118 , TYR A:120 , LYS A:122 , GLY A:123 , GLN A:124 , MET A:125 , SER A:126 , THR A:164 , THR A:167 , HOH A:1607 , HOH A:1610 , HOH A:1611 , HOH A:1614 , HOH A:1615 , HOH A:1618 , HOH A:1646 , HOH A:1714 , HOH A:1814 , HOH A:1864 , PHE B:233 , VAL B:234 , MET B:259 , LYS B:262 , ALA B:263 , MET B:264 , HIS B:267 , GOL B:1401BINDING SITE FOR RESIDUE FAD A 1301
7AC7SOFTWAREPHE A:233 , VAL A:234 , MET A:259 , LYS A:262 , ALA A:263 , MET A:264 , HIS A:267 , GOL A:1402 , ARG B:99 , PRO B:100 , TYR B:101 , THR B:102 , ILE B:116 , ILE B:117 , LYS B:118 , TYR B:120 , LYS B:122 , GLY B:123 , GLN B:124 , MET B:125 , SER B:126 , THR B:164 , THR B:167 , PHE B:281 , HOH B:1603 , HOH B:1608 , HOH B:1617 , HOH B:1628 , HOH B:1633 , HOH B:1640 , HOH B:1654 , HOH B:1674 , HOH B:1711 , HOH B:1802BINDING SITE FOR RESIDUE FAD B 1302
8AC8SOFTWARETYR A:120 , PRO A:257 , FAD A:1301 , MET B:259 , LYS B:262 , HOH B:1789BINDING SITE FOR RESIDUE GOL B 1401
9AC9SOFTWAREMET A:259 , LYS A:262 , HOH A:1818 , TYR B:120 , FAD B:1302BINDING SITE FOR RESIDUE GOL A 1402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EIX)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:142 -Pro A:143
2Gly B:142 -Pro B:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EIX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EIX)

(-) Exons   (0, 0)

(no "Exon" information available for 2EIX)

(-) 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:243
 aligned with Q1HA49_PHYPO | Q1HA49 from UniProtKB/TrEMBL  Length:281

    Alignment length:243
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278   
         Q1HA49_PHYPO    39 KREPALNPNEYKKFMLREKQIINHNTRLFRFNLHHPEDVVGLPIGQHMSVKATVDGKEIYRPYTPVSSDDEKGYFDLIIKVYEKGQMSQYIDHLNPGDFLQVRGPKGQFDYKPNMVKEMGMIAGGTGITPMLQVARAIIKNPKEKTIINLIFANVNEDDILLRTELDDMAKKYSNFKVYYVLNNPPAGWTGGVGFVSADMIKQHFSPPSSDIKVMMCGPPMMNKAMQGHLETLGYTPEQWFIF 281
               SCOP domains d2eixa1 A:39-150 automated matches                                                                              d2eixa2 A:151-281 automated matches                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeeee..eeeeeee..............eeeeeeee..eeeeeee..........eeeeeee....hhhhhhhhh.....eeeeeeee...........eeeeeee..hhhhhhhhhhhhhh......eeeeeeeeee.hhh.hhhhhhhhhhhh..eeeeeeeee.......ee...hhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhh.hhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2eix A  39 KREPALNPNEYKKFMLREKQIINHNTRLFRFNLHHPEDVVGLPIGQHMSVKATVDGKEIYRPYTPVSSDDEKGYFDLIIKVYEKGQMSQYIDHLNPGDFLQVRGPKGQFDYKPNMVKEMGMIAGGTGITPMLQVARAIIKNPKEKTIINLIFANVNEDDILLRTELDDMAKKYSNFKVYYVLNNPPAGWTGGVGFVSADMIKQHFSPPSSDIKVMMCGPPMMNKAMQGHLETLGYTPEQWFIF 281
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278   


Chain B from PDB  Type:PROTEIN  Length:243
 aligned with Q1HA49_PHYPO | Q1HA49 from UniProtKB/TrEMBL  Length:281

    Alignment length:243
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278   
         Q1HA49_PHYPO    39 KREPALNPNEYKKFMLREKQIINHNTRLFRFNLHHPEDVVGLPIGQHMSVKATVDGKEIYRPYTPVSSDDEKGYFDLIIKVYEKGQMSQYIDHLNPGDFLQVRGPKGQFDYKPNMVKEMGMIAGGTGITPMLQVARAIIKNPKEKTIINLIFANVNEDDILLRTELDDMAKKYSNFKVYYVLNNPPAGWTGGVGFVSADMIKQHFSPPSSDIKVMMCGPPMMNKAMQGHLETLGYTPEQWFIF 281
               SCOP domains d2eixb1 B:39-150 automated matches                                                                              d2eixb2 B:151-281 automated matches                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeeee..eeeeeee..............eeeeeeee..eeeeeee..........eeeeeee....hhhhhhhhh.....eeeeeeee...........eeeeeee..hhhhhhhhhhhhhhh.....eeeeeeeeee.hhh.hhhhhhhhhhhh..eeeeeeeee.......ee...hhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhh.hhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2eix B  39 KREPALNPNEYKKFMLREKQIINHNTRLFRFNLHHPEDVVGLPIGQHMSVKATVDGKEIYRPYTPVSSDDEKGYFDLIIKVYEKGQMSQYIDHLNPGDFLQVRGPKGQFDYKPNMVKEMGMIAGGTGITPMLQVARAIIKNPKEKTIINLIFANVNEDDILLRTELDDMAKKYSNFKVYYVLNNPPAGWTGGVGFVSADMIKQHFSPPSSDIKVMMCGPPMMNKAMQGHLETLGYTPEQWFIF 281
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278
   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, 4)

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 2EIX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EIX)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q1HA49_PHYPO | Q1HA49)
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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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: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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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1umk THE STRUCTURE OF HUMAN ERYTHROCYTE NADH-CYTOCHROME B5 REDUCTASE