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(-) Description

Title :  CRYSTAL STRUCTURE OF PYRIDOXAMINE 5'-PHOSPHATE OXIDASE-LIKE PROTEIN (NP_783940.1) FROM LACTOBACILLUS PLANTARUM AT 1.55 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  07 Nov 07  (Deposition) - 20 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Np_783940. 1, Pyridoxamine 5'-Phosphate Oxidase-Like Protein, 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 Pyridoxamine 5'-Phosphate Oxidase-Like Protein (Np_783940. 1) From Lactobacillus Plantarum At 1. 55 Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PYRIDOXAMINE 5'-PHOSPHATE OXIDASE-LIKE PROTEIN
    Atcc: BAA-793
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_783940.1, LP_0091
    Organism Scientific: LACTOBACILLUS PLANTARUM WCFS1
    Organism Taxid: 220668
    Strain: WCFS1, NCIMB 8826
    Synonym: PROTEIN LP_0091

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:133 , VAL A:134 , GLY A:135 , LYS A:138 , EDO A:149 , LYS B:138 , HOH B:180 , HOH B:383BINDING SITE FOR RESIDUE SO4 A 145
02AC2SOFTWAREASN A:14 , LYS A:15 , PRO A:105 , HOH A:169 , HOH A:191 , HOH A:197 , HOH A:222 , HOH A:274 , HOH A:318 , HOH B:297BINDING SITE FOR RESIDUE SO4 A 146
03AC3SOFTWAREASP B:112 , ALA B:113 , ILE B:114 , GLY B:115 , SER B:116 , HOH B:217 , HOH B:312 , HOH B:327BINDING SITE FOR RESIDUE EDO B 145
04AC4SOFTWAREASP A:112 , ALA A:113 , ILE A:114 , GLY A:115 , SER A:116 , HOH A:236 , HOH A:283BINDING SITE FOR RESIDUE EDO A 147
05AC5SOFTWARETYR B:36 , LYS B:91 , ASP B:95 , EDO B:148BINDING SITE FOR RESIDUE EDO B 146
06AC6SOFTWARELYS B:15 , ASN B:32 , HOH B:289 , HOH B:291 , HOH B:315BINDING SITE FOR RESIDUE EDO B 147
07AC7SOFTWARELYS A:15 , ILE A:30 , HOH A:169 , HOH A:195 , ASN B:76BINDING SITE FOR RESIDUE EDO A 148
08AC8SOFTWARELYS A:29 , GLY A:135 , GLY A:136 , SO4 A:145BINDING SITE FOR RESIDUE EDO A 149
09AC9SOFTWARETYR A:36 , LYS A:91 , ASP A:95 , HOH A:293 , HOH A:300BINDING SITE FOR RESIDUE EDO A 150
10BC1SOFTWARELEU A:101 , GLU A:102 , THR A:103 , PRO A:105 , HOH A:207 , HOH A:301BINDING SITE FOR RESIDUE EDO A 151
11BC2SOFTWAREALA B:38 , GLN B:39 , TYR B:44 , EDO B:146 , HOH B:336BINDING SITE FOR RESIDUE EDO B 148
12BC3SOFTWAREHOH A:205 , LYS B:29 , GLU B:137 , GLN B:139BINDING SITE FOR RESIDUE EDO A 152

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BA3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BA3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BA3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BA3)

(-) Exons   (0, 0)

(no "Exon" information available for 3BA3)

(-) 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:143
 aligned with F9USS0_LACPL | F9USS0 from UniProtKB/TrEMBL  Length:144

    Alignment length:143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   
         F9USS0_LACPL     1 MDISLLKQVVQSTNKIALSTAVNNEADVKIVNFVWYEAQPDTLYFSSVKTSPALKVYDQNPDIAFITIPNDGTAGNPYLRAQHVKLQRSTKTMTDLLPQYLETVPNYQQVWDAIGSTLVVFELKLTDLFVDAGVGGEKQTLTF 143
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3ba3A00 A:2-143 Electron Transport, Fmn-binding Protein; Chain A                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhheeeeeeeeee..eeeeeeee.ee......eeeeeee...hhhhhhh...eeeeeeee........eeeeeeeeeee...hhhhhhhhhhhhh.hhhhhhhhhh..eeeeeee..eeeee......eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ba3 A   1 mDISLLKQVVQSTNKIALSTAVNNEADVKIVNFVWYEAQPDTLYFSSVKTSPALKVYDQNPDIAFITIPNDGTAGNPYLRAQHVKLQRSTKTmTDLLPQYLETVPNYQQVWDAIGSTLVVFELKLTDLFVDAGVGGEKQTLTF 143
                            |       10        20        30        40        50        60        70        80        90  |    100       110       120       130       140   
                            |                                                                                          93-MSE                                              
                            1-MSE                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:144
 aligned with F9USS0_LACPL | F9USS0 from UniProtKB/TrEMBL  Length:144

    Alignment length:144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    
         F9USS0_LACPL     1 MDISLLKQVVQSTNKIALSTAVNNEADVKIVNFVWYEAQPDTLYFSSVKTSPALKVYDQNPDIAFITIPNDGTAGNPYLRAQHVKLQRSTKTMTDLLPQYLETVPNYQQVWDAIGSTLVVFELKLTDLFVDAGVGGEKQTLTFN 144
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains -3ba3B00 B:2-144 Electron Transport, Fmn-binding Protein; Chain A                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhh.eeeeeeeehhhhh.eeeeee.........eeeeeee....hhhhhh...eeeeeeee........eeeeeeeeeee...hhhhhhhhhhhhh.hhhhhhhhhh..eeeeeee..eeeee......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ba3 B   1 mDISLLKQVVQSTNKIALSTAVNNEADVKIVNFVWYEAQPDTLYFSSVKTSPALKVYDQNPDIAFITIPNDGTAGNPYLRAQHVKLQRSTKTmTDLLPQYLETVPNYQQVWDAIGSTLVVFELKLTDLFVDAGVGGEKQTLTFN 144
                            |       10        20        30        40        50        60        70        80        90  |    100       110       120       130       140    
                            1-MSE                                                                                      93-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  (0, 0)

(no "SCOP Domain" information available for 3BA3)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BA3)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (F9USS0_LACPL | F9USS0)
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.
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.

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