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(-) Description

Title :  CRYSTAL STRUCTURE OF UNCHARACTERIZED PROTEIN JW3007 FROM ESCHERICHIA COLI K12
 
Authors :  M. G. Newton, Y. Takagi, A. Ebihara, A. Shinkai, S. Kuramitsu, S. Yokaya L. Chen, J. Zhu, J. Ruble, Z. J. Liu, J. P. Rose, B-C. Wang, Southeast Collaboratory For Structural Genomics (Secsg), Riken Structu Genomics/Proteomics Initiative (Rsgi)
Date :  10 May 07  (Deposition) - 12 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Jw3007, Uncharacterized Protein, Escherichia Coli Structural Genomics, Protein Structure, Riken And Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. G. Newton, Y. Takagi, A. Ebihara, A. Shinkai, S. Kuramitsu, S. Yokayama, Y. Li, L. Chen, J. Zhu, J. Ruble, Z. J. Liu, J. P. Rose, B-C. Wang
Crystal Structure Of Uncharacterized Protein Jw3007 From Escherichia Coli K12.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN YGID
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCR2.1-TOPO
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YGID, B3039, JW3007
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2ZN3Ligand/IonZINC ION
Biological Unit 1 (1, 20)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:22 , HIS A:57 , ASP A:86 , HIS A:234 , HOH A:277BINDING SITE FOR RESIDUE ZN A 272
2AC2SOFTWAREHIS A:121BINDING SITE FOR RESIDUE ZN A 273
3AC3SOFTWAREHIS A:177BINDING SITE FOR RESIDUE ZN A 274

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PW6)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:27 -Val A:28
2Ala A:106 -Pro A:107
3Gly A:186 -Asp A:187
4Glu A:223 -Gly A:224

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PW6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PW6)

(-) Exons   (0, 0)

(no "Exon" information available for 2PW6)

(-) 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:244
 aligned with YGID_ECOLI | P24197 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:258
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263        
           YGID_ECOLI    14 RMPALFLGHGSPMNVLEDNLYTRSWQKLGMTLPRPQAIVVVSAHWFTRGTGVTAMETPPTIHDFGGFPQALYDTHYPAPGSPALAQRLVELLAPIPVTLDKEAWGFDHGSWGVLIKMYPDADIPMVQLSIDSSKPAAWHFEMGRKLAALRDEGIMLVASGNVVHNLRTVKWHGDSSPYPWATSFNEYVKANLTWQGPVEQHPLVNYLDHEGGTLSNPTPEHYLPLLYVLGAWDGQEPITIPVEGIEMGSLSMLSVQIG 271
               SCOP domains d2pw6a1 A: 14-271 Uncharacterized protein YgiD                                                                                                                                                                                                                     SCOP domains
               CATH domains 2pw6A00 A: 14-271 Protocatechuate 4,5-dioxygenase; Chain              B                                                                                                                                                                                            CATH domains
               Pfam domains LigB-2pw6A 01 A:14-262                                                                                                                                                                                                                                   --------- Pfam domains
         Sec.struct. author ...eeeee..-.......hhhhhhhhhhhhhh....eeeeeeeeeee..eeee....-------------..........hhhhhhhhhhhhh...eeee......hhhhhhhhhhhh......eeeeeee...hhhhhhhhhhhhhhhhhh.eeeeeee.................hhhhhhhhhhhhh......hhhhh...hhhhh.hhhhhh.....hhhhhhhhhh......ee.....ee...ee...eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pw6 A  14 RmPALFLGHG-PmNVLEDNLYTRSWQKLGmTLPRPQAIVVVSAHWFTRGTGVTAmET-------------LYDTHYPAPGSPALAQRLVELLAPIPVTLDKEAWGFDHGSWGVLIKmYPDADIPmVQLSIDSSKPAAWHFEmGRKLAALRDEGImLVASGNVVHNLRTVKWHGDSSPYPWATSFNEYVKANLTWQGPVEQHPLVNYLDHEGGTLSNPTPEHYLPLLYVLGAWDGQEPITIPVEGIEmGSLSmLSVQIG 271
                             |      23 ||     33        43        53        63    | |  -         -|       93       103       113       123      |133    |  143       153 |     163    |  173       183       193       203       213       223       233       243       253      |263 |      
                             |      23 ||               43-MSE                   68-MSE          84                                           130-MSE 138-MSE          155-MSE      168-MSE                                                                                     260-MSE|      
                            15-MSE    25|                                          70                                                                                                                                                                                                265-MSE  
                                       26-MSE
   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) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: LigB (1)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (YGID_ECOLI | P24197)
molecular function
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    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:0016701    oxidoreductase activity, acting on single donors with incorporation of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and molecular oxygen is incorporated into a donor.
    GO:0050297    stizolobate synthase activity    Catalysis of the reaction: 3,4-dihydroxy-L-phenylalanine + O2 = 4-(L-alanin-3-yl)-2-hydroxy-cis,cis-muconate 6-semialdehyde.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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