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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE PYRIDOXAMINE 5'-PHOSPHATE OXIDASE (LDB0262) FROM LACTOBACILLUS DELBRUECKII SUBSP. AT 1.60 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  25 Jul 06  (Deposition) - 15 Aug 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Putative Pyridoxamine 5'-Phosphate Oxidase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Predicted Flavin-Nucleotide-Binding Protein From Cog3576 Family Structurally Related To Pyridoxine 5'-Phosphate Oxidase (Zp_00387536. 1) From Lactobacillus Delbrueckii Bulgaricus Atcc Baa-365 At 1. 60 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PREDICTED FLAVIN-NUCLEOTIDE-BINDING PROTEIN FROM COG3576 FAMILY STRUCTURALLY RELATED TO PYRIDOXINE 5'-PHOSPHATE OXIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ZP_00387536.1
    Organism Scientific: LACTOBACILLUS DELBRUECKII SUBSP. BULGARICUS
    Organism Taxid: 321956
    Strain: ATCC BAA-365

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MSE4Mod. Amino AcidSELENOMETHIONINE
3SO46Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:11BINDING SITE FOR RESIDUE CL B 122
2AC2SOFTWAREHOH A:189 , HOH A:206 , GLY B:39 , SER B:40 , LYS B:54 , HOH B:178 , HOH B:182BINDING SITE FOR RESIDUE SO4 B 123
3AC3SOFTWAREMSE A:1 , ARG A:83 , THR B:55 , GLY B:57 , GLU B:58 , ALA B:59BINDING SITE FOR RESIDUE SO4 A 122
4AC4SOFTWARETHR A:6 , ASN A:7 , LYS A:8 , HOH A:167BINDING SITE FOR RESIDUE SO4 A 123
5AC5SOFTWAREGLN A:34 , GLU A:58 , ALA A:59 , HOH A:143 , HOH A:164 , HOH A:186 , GLY B:0 , MSE B:1 , ARG B:83BINDING SITE FOR RESIDUE SO4 A 124
6AC6SOFTWARELYS A:38 , GLY A:39 , SER A:40 , LYS A:54 , HOH A:175 , HOH A:205 , HOH B:188BINDING SITE FOR RESIDUE SO4 A 125
7AC7SOFTWARELEU A:44 , TYR A:96 , HOH A:180 , HOH A:238 , HOH A:239BINDING SITE FOR RESIDUE SO4 A 126

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HTD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2HTD)

(-) 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:122
 aligned with Q1GBW8_LACDA | Q1GBW8 from UniProtKB/TrEMBL  Length:121

    Alignment length:122
                             1                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119  
         Q1GBW8_LACDA     - -MKKLNTNKLTEEQVNLFKNNLVYLATVDAEGNPQVGPKGSMTVLDPSHLQYLEKTKGEAYENIKRGSKVALVAADVPSHTAVRVLATAEVHEDDDYAKKVLAKTEFPNAFVVNLNIEEVFA 121
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2htdA00 A:0-121 Electron Transport, Fmn-binding Protein; Chain A                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......hhhhhhhhhhh.eeeeee.....eeeeee...eeee..eeeeee...hhhhhhhhh...eeeeeee....eeeeeeeeeeee..hhhhhhhhh.......eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2htd A   0 GmKKLNTNKLTEEQVNLFKNNLVYLATVDADGNPQVGPKGSmTVLDPSHLQYLEKTKGEAYENIKRGSKVALVAADVPSHTAVRVLATAEVHEDDDYAKKVLAKTEFPNAFVVNLNIEEVFA 121
                             |       9        19        29        39 |      49        59        69        79        89        99       109       119  
                             |                                      41-MSE                                                                            
                             1-MSE                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:124
 aligned with Q1GBW8_LACDA | Q1GBW8 from UniProtKB/TrEMBL  Length:121

    Alignment length:124
                               1                                                                                                                        
                               |     7        17        27        37        47        57        67        77        87        97       107       117    
         Q1GBW8_LACDA     - ---MKKLNTNKLTEEQVNLFKNNLVYLATVDAEGNPQVGPKGSMTVLDPSHLQYLEKTKGEAYENIKRGSKVALVAADVPSHTAVRVLATAEVHEDDDYAKKVLAKTEFPNAFVVNLNIEEVFA 121
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2htdB00 B:-2-121 Electron Transport, Fmn-binding Protein; Chain A                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee......hhhhhhhhhhh.eeeeee.....eeeeee...eeee..eeeeee...hhhhhhhhh...eeeeeee....eeeeeeeeeeee..hhhhhhhhh.......eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 2htd B  -2 FQGmKKLNTNKLTEEQVNLFKNNLVYLATVDADGNPQVGPKGSmTVLDPSHLQYLEKTKGEAYENIKRGSKVALVAADVPSHTAVRVLATAEVHEDDDYAKKVLAKTEFPNAFVVNLNIEEVFA 121
                               |     7        17        27        37   |    47        57        67        77        87        97       107       117    
                               1-MSE                                  41-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "SCOP Domain" information available for 2HTD)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q1GBW8_LACDA | Q1GBW8)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    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:0004733    pyridoxamine-phosphate oxidase activity    Catalysis of the reaction: pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + hydrogen peroxide.
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:0042823    pyridoxal phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.

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