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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE PROTOPORPHYRINOGEN OXIDASE (YP_001813199.1) FROM EXIGUOBACTERIUM SP. 255-15 AT 2.06 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  04 Feb 10  (Deposition) - 23 Feb 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym./Biol. Unit :  A
Keywords :  Putative Protoporphyrinogen Oxidase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Flavin Containing Amine Oxidoreductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Protoporphyrinogen Oxidase (Yp_001813199. 1) From Exiguobacterium Sp. 255-15 At 2. 06 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTOPORPHYRINOGEN OXIDASE
    Chains: A
    EC Number: 1.3.3.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: EXIG_0701
    Organism Scientific: EXIGUOBACTERIUM SIBIRICUM
    Organism Taxid: 262543
    Strain: DSM 17290 / JCM 13490 / 255-15

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:9 , GLY A:10 , GLY A:12 , ILE A:13 , THR A:14 , LEU A:34 , GLU A:35 , ALA A:36 , GLY A:42 , LYS A:43 , PRO A:58 , ASP A:59 , SER A:60 , TYR A:174 , PRO A:255 , LEU A:256 , ILE A:284 , PRO A:285 , GLN A:288 , THR A:309 , LEU A:409 , GLY A:438 , LEU A:439 , VAL A:444 , GLY A:445 , LEU A:446 , CYS A:449 , HOH A:475 , HOH A:479 , HOH A:481 , HOH A:484 , HOH A:487 , HOH A:494 , HOH A:598 , HOH A:623 , HOH A:634BINDING SITE FOR RESIDUE FAD A 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LOV)

(-) 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:451
 aligned with B1YKJ9_EXIS2 | B1YKJ9 from UniProtKB/TrEMBL  Length:474

    Alignment length:465
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459     
         B1YKJ9_EXIS2     - -MSSKRLVIVGGGITGLAAAYYAERAFPDLNITLLEAGERLGGKVATYREDGFTIERGPDSYVARKHILTDLIEAIGLGEKLVRNNTSQAFILDTGGLHPIPKGAVMGIPTDLDLFRQTTLLTEEEKQEVADLLLHPSDSLRIPEQDIPLGEYLRPRLGDALVEKLIEPLLSGIYAGNIDQMSTFATYPQFVANEQKAGSLFEGMRLMRPLDQLPQTPQTTIKATGQFLSLETGLESLIERLEEVLERSEIRLETPLLAISREDGRYRLKTDHGPEYADYVLLTIPHPQVVQLLPDAHLPELEQLTTHSTATVTMIFDQQQSLPIEGTGFVVNRRAPYSITACTAIDQKWNHSAPDHTVLRAFVGRPGNDHLVHESDEVLQQAVLQDLEKICGRTLEPKQVIISRLMDGLPAYTVGHADRIQRVREEVLAQYPGIYLAGLAYDGVGLPDCVASAKTMIESIELEQ 464
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------Amino_oxidase-3lovA01 A:13-456                                                                                                                                                                                                                                                                                                                                                                                                                              -------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhhh...eeeee...........ee......ee.....ee...hhhhhhhhhh.hhh.eee.....eeeee..eeee....ee..ee.hhhhhh.....hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh..--------------...eeee..hhhhhhhhhhhhh...eee......eeeee..eeeee.....eee.eeee..hhhhhhhhh....hhhhhh..eeeeeeeeeeee..........eeee.......eeeeeehhhhh......eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeeeee....hhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lov A   0 GmSSKRLVIVGGGITGLAAAYYAERAFPDLNITLLEAGERLGGKVATYREDGFTIERGPDSYVARKHILTDLIEAIGLGEKLVRNNTSQAFILDTGGLHPIPKGAVmGIPTDLDLFRQTTLLTEEEKQEVADLLLHPSDSLRIPEQDIPLGEYLRPRLGDALVEKLIEPLLSGIYAGNIDQmSTFATYPQFVANEQKAGSLFEGmRLmRP--------------TGQFLSLETGLESLIERLEEVLERSEIRLETPLLAISREDGRYRLKTDHGPEYADYVLLTIPHPQVVQLLPDAHLPELEQLTTHSTATVTmIFDQQQSLPIEGTGFVVNRRAPYSITACTAIDQKWNHSAPDHTVLRAFVGRPGNDHLVHESDEVLQQAVLQDLEKICGRTLEPKQVIISRLmDGLPAYTVGHADRIQRVREEVLAQYPGIYLAGLAYDGVGLPDCVASAKTmIESIELEQ 464
                             |       9        19        29        39        49        59        69        79        89        99      |109       119       129       139       149       159       169       179 |     189       199    |  209         -    |  229       239       249       259       269       279       289       299       309    |  319       329       339       349       359       369       379       389       399      |409       419       429       439       449      |459     
                             |                                                                                                      106-MSE                                                                    181-MSE                204-MSE|            224                                                                                       314-MSE                                                                                     406-MSE                                           456-MSE    
                             1-MSE                                                                                                                                                                                                       207-MSE                                                                                                                                                                                                                                                             
                                                                                                                                                                                                                                           209
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  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 3LOV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LOV)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (B1YKJ9_EXIS2 | B1YKJ9)
molecular function
    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.
    GO:0004729    oxygen-dependent protoporphyrinogen oxidase activity    Catalysis of the reaction: 3 O(2) + protoporphyrinogen IX = 3 H(2)O(2) + protoporphyrin IX.
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:0006779    porphyrin-containing compound biosynthetic process    The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.

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