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(-) Description

Title :  CRYSTAL STRUCTURE OF YGIN IN COMPLEX WITH MENADIONE
 
Authors :  M. A. Adams, Z. Jia
Date :  25 Jun 04  (Deposition) - 11 Jan 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  A  (1x)
Keywords :  Menadione Oxidase, Monooxygenase, Co-Crystal With Natural Product, Ferredoxin Fold, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Adams, Z. Jia
Structural And Biochemical Evidence For An Enzymatic Quinon Redox Cycle In Escherichia Coli: Identification Of A Novel Quinol Monooxygenase
J. Biol. Chem. V. 280 8358 2005
PubMed-ID: 15613473  |  Reference-DOI: 10.1074/JBC.M412637200

(-) Compounds

Molecule 1 - PROTEIN YGIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: YGIN
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (2x): A
Biological Unit 3 (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1VK31Ligand/IonMENADIONE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1VK32Ligand/IonMENADIONE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1VK32Ligand/IonMENADIONE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1VK31Ligand/IonMENADIONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:40 , SER A:51 , GLU A:64 , HIS A:75 , LEU A:76 , TYR A:84 , MET A:95 , ILE A:97 , HOH A:4651BINDING SITE FOR RESIDUE VK3 A 4558

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TUV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ABMPS51725 ABM domain profile.YGIN_ECO572-100  1A:2-100
YGIN_ECOLI2-100  1A:2-100
YGIN_SHIFL2-100  1A:2-100
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ABMPS51725 ABM domain profile.YGIN_ECO572-100  2A:2-100
YGIN_ECOLI2-100  2A:2-100
YGIN_SHIFL2-100  2A:2-100
Biological Unit 2 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ABMPS51725 ABM domain profile.YGIN_ECO572-100  2A:2-100
YGIN_ECOLI2-100  2A:2-100
YGIN_SHIFL2-100  2A:2-100
Biological Unit 3 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ABMPS51725 ABM domain profile.YGIN_ECO572-100  1A:2-100
YGIN_ECOLI2-100  1A:2-100
YGIN_SHIFL2-100  1A:2-100

(-) Exons   (0, 0)

(no "Exon" information available for 1TUV)

(-) Sequences/Alignments

Asymmetric 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:103
 aligned with YGIN_ECO57 | P0ADU3 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:103
                                    10        20        30        40        50        60        70        80        90       100   
           YGIN_ECO57     1 MLTVIAEIRTRPGQHHRQAVLDQFAKIVPTVLKEEGCHGYAPMVDCAAGVSFQSMAPDSIVMIEQWESIAHLEAHLQTPHMKAYSEAVKGDVLEMNIRILQPG 103
               SCOP domains d1tuva_ A: Hypothetical protein YgiN                                                                    SCOP domains
               CATH domains 1tuvA00 A:1-103  [code=3.30.70.900, no name defined]                                                    CATH domains
               Pfam domains ABM-1tuvA01 A:1-87                                                                     ---------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhhhhhhhhhh..eeeeeee...............eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ABM  PDB: A:2-100 UniProt: 2-100                                                                   --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1tuv A   1 MLTVIAEIRTRPGQHHRQAVLDQFAKIVPTVLKEEGCHGYAPMVDCAAGVSFQSMAPDSIVMIEQWESIAHLEAHLQTPHMKAYSEAVKGDVLEMNIRILQPG 103
                                    10        20        30        40        50        60        70        80        90       100   


Chain A from PDB  Type:PROTEIN  Length:103
 aligned with YGIN_ECOLI | P0ADU2 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:103
                                    10        20        30        40        50        60        70        80        90       100   
           YGIN_ECOLI     1 MLTVIAEIRTRPGQHHRQAVLDQFAKIVPTVLKEEGCHGYAPMVDCAAGVSFQSMAPDSIVMIEQWESIAHLEAHLQTPHMKAYSEAVKGDVLEMNIRILQPG 103
               SCOP domains d1tuva_ A: Hypothetical protein YgiN                                                                    SCOP domains
               CATH domains 1tuvA00 A:1-103  [code=3.30.70.900, no name defined]                                                    CATH domains
               Pfam domains ABM-1tuvA01 A:1-87                                                                     ---------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhhhhhhhhhh..eeeeeee...............eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -ABM  PDB: A:2-100 UniProt: 2-100                                                                   --- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1tuv A   1 MLTVIAEIRTRPGQHHRQAVLDQFAKIVPTVLKEEGCHGYAPMVDCAAGVSFQSMAPDSIVMIEQWESIAHLEAHLQTPHMKAYSEAVKGDVLEMNIRILQPG 103
                                    10        20        30        40        50        60        70        80        90       100   


Chain A from PDB  Type:PROTEIN  Length:103
 aligned with YGIN_SHIFL | P0ADU4 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:103
                                    10        20        30        40        50        60        70        80        90       100   
           YGIN_SHIFL     1 MLTVIAEIRTRPGQHHRQAVLDQFAKIVPTVLKEEGCHGYAPMVDCAAGVSFQSMAPDSIVMIEQWESIAHLEAHLQTPHMKAYSEAVKGDVLEMNIRILQPG 103
               SCOP domains d1tuva_ A: Hypothetical protein YgiN                                                                    SCOP domains
               CATH domains 1tuvA00 A:1-103  [code=3.30.70.900, no name defined]                                                    CATH domains
               Pfam domains ABM-1tuvA01 A:1-87                                                                     ---------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhhhhhhhhhh..eeeeeee...............eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -ABM  PDB: A:2-100 UniProt: 2-100                                                                   --- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1tuv A   1 MLTVIAEIRTRPGQHHRQAVLDQFAKIVPTVLKEEGCHGYAPMVDCAAGVSFQSMAPDSIVMIEQWESIAHLEAHLQTPHMKAYSEAVKGDVLEMNIRILQPG 103
                                    10        20        30        40        50        60        70        80        90       100
   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  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Dim_A_B_barrel (36)

(-) Gene Ontology  (4, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (YGIN_ECO57 | P0ADU3)
molecular function
    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.

Chain A   (YGIN_SHIFL | P0ADU4)
molecular function
    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.

Chain A   (YGIN_ECOLI | P0ADU2)
molecular function
    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.
    GO:0010447    response to acidic pH    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus with pH < 7. pH is a measure of the acidity or basicity of an aqueous solution.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Databases and Analysis Tools

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  1tuv
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  YGIN_ECO57 | P0ADU3
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  YGIN_ECOLI | P0ADU2
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  YGIN_SHIFL | P0ADU4
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 Related Entries

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

UniProtKB/Swiss-Prot
        YGIN_ECO57 | P0ADU3: 1r6y
        YGIN_ECOLI | P0ADU2: 1r6y
        YGIN_SHIFL | P0ADU4: 1r6y

(-) Related Entries Specified in the PDB File

1r6y NATIVE, UNCOMPLEXED PROTEIN