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(-) Description

Title :  CRYSTAL STRUCTURE OF A PYRIDOXAMINE 5'-PHOSPHATE OXIDASE-RELATED FMN-BINDING PROTEIN (JANN_0254) FROM JANNASCHIA SP. CCS1 AT 1.60 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  09 Feb 07  (Deposition) - 06 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Split Barrel-Like Fold, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Flavoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Pyridoxamine 5'-Phosphate Oxidase-Related Fmn-Binding (Yp_508196. 1) From Jannaschia Sp. Ccs1 At 1. 60 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PYRIDOXAMINE 5'-PHOSPHATE OXIDASE-RELATED, FMN-BINDING
    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: YP_508196.1, JANN_0254
    Organism Scientific: JANNASCHIA SP.
    Organism Taxid: 290400
    Strain: CCS1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2GOL4Ligand/IonGLYCEROL
3MSE4Mod. Amino AcidSELENOMETHIONINE
4SO41Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:0 , MSE A:1 , SER A:2 , VAL A:5 , HOH A:419 , ARG B:168 , HOH B:446BINDING SITE FOR RESIDUE SO4 A 175
2AC2SOFTWAREHIS A:30 , ARG A:44 , THR A:45 , LEU A:46 , VAL A:47 , HIS A:61 , THR A:62 , SER A:66 , PRO A:67 , LYS A:68 , HOH A:309 , HOH A:312 , HOH A:330 , HOH A:344 , HOH A:364 , HOH A:467 , HOH A:499 , TRP B:83 , GLN B:90 , ARG B:92 , ARG B:159BINDING SITE FOR RESIDUE FMN A 300
3AC3SOFTWARETRP A:83 , GLN A:90 , ARG A:92 , LEU A:153 , HOH A:323 , HIS B:30 , ARG B:44 , THR B:45 , LEU B:46 , VAL B:47 , HIS B:61 , THR B:62 , SER B:66 , PRO B:67 , LYS B:68 , HOH B:304 , HOH B:308 , HOH B:332 , HOH B:379 , HOH B:392 , HOH B:402BINDING SITE FOR RESIDUE FMN B 300
4AC4SOFTWAREARG A:49 , ALA A:114 , HOH A:426BINDING SITE FOR RESIDUE GOL A 301
5AC5SOFTWAREARG B:24 , ARG B:29 , ARG B:49 , PRO B:101 , HOH B:398BINDING SITE FOR RESIDUE GOL B 301
6AC6SOFTWARETRP A:83 , HIS B:25 , HIS B:26 , PRO B:27 , HIS B:30 , HOH B:461BINDING SITE FOR RESIDUE GOL B 302
7AC7SOFTWAREPRO A:111 , GLU A:112 , GLN B:15 , ARG B:19 , LYS B:22 , HOH B:390BINDING SITE FOR RESIDUE GOL B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OU5)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Leu A:127 -Pro A:128
2Thr A:155 -Pro A:156
3Ala A:164 -Pro A:165
4Leu B:127 -Pro B:128
5Thr B:155 -Pro B:156
6Ala B:164 -Pro B:165

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OU5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OU5)

(-) Exons   (0, 0)

(no "Exon" information available for 2OU5)

(-) 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:175
 aligned with Q28VU1_JANSC | Q28VU1 from UniProtKB/TrEMBL  Length:174

    Alignment length:175
                             1                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169     
         Q28VU1_JANSC     - -MSDTVLTGLLDTVWQQFGRGTKDRHHPARHPTLATIGTDGPDLRTLVLRAASHAEATLEFHTDAASPKVAHIRRDARVAIHIWIPKASLQVRAKAIAKILPGDPNLFAQLPEAARMNYQGPVPGTPLPAEPDATPNRFTRLICHLSEIDVLHLTTPHQRAVYTAPDWRGIWVSP 174
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ou5A00 A:0-174 Electron Transport, Fmn-binding Protein; Chain A                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeee..eeeeee....eee....eeeeeee..hhhhhhhhhh.eeeeeeeehhh.eeeeeeeeeeeee.hhhhhhhhhhhhhhhhh..................eeeeeeeeeeeeeee.....eeeeee......eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ou5 A   0 GmSDTVLTGLLDTVWQQFGRGTKDRHHPARHPTLATIGTDGPDLRTLVLRAASHAEATLEFHTDAASPKVAHIRRDARVAIHIWIPKASLQVRAKAIAKILPGDPNLFAQLPEAARmNYQGPVPGTPLPAEPDATPNRFTRLICHLSEIDVLHLTTPHQRAVYTAPDWRGIWVSP 174
                             |       9        19        29        39        49        59        69        79        89        99       109      |119       129       139       149       159       169     
                             |                                                                                                                116-MSE                                                      
                             1-MSE                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:175
 aligned with Q28VU1_JANSC | Q28VU1 from UniProtKB/TrEMBL  Length:174

    Alignment length:175
                             1                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169     
         Q28VU1_JANSC     - -MSDTVLTGLLDTVWQQFGRGTKDRHHPARHPTLATIGTDGPDLRTLVLRAASHAEATLEFHTDAASPKVAHIRRDARVAIHIWIPKASLQVRAKAIAKILPGDPNLFAQLPEAARMNYQGPVPGTPLPAEPDATPNRFTRLICHLSEIDVLHLTTPHQRAVYTAPDWRGIWVSP 174
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ou5B00 B:0-174 Electron Transport, Fmn-binding Protein; Chain A                                                                                                                CATH domains
           Pfam domains (1) -----------Pyridox_oxase_2-2ou5B01 B:11-101                                                           ------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------Pyridox_oxase_2-2ou5B02 B:11-101                                                           ------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeee..eeeeee..eeeee....eeeeeee..hhhhhhhhhh.eeeeeeeehhh.eeeeeeeeeeeee.hhhhhhhhhhhhhhhh...............hhh.eeeeeeeeeeeeeee.....eeeeee......eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ou5 B   0 GmSDTVLTGLLDTVWQQFGRGTKDRHHPARHPTLATIGTDGPDLRTLVLRAASHAEATLEFHTDAASPKVAHIRRDARVAIHIWIPKASLQVRAKAIAKILPGDPNLFAQLPEAARmNYQGPVPGTPLPAEPDATPNRFTRLICHLSEIDVLHLTTPHQRAVYTAPDWRGIWVSP 174
                             |       9        19        29        39        49        59        69        79        89        99       109      |119       129       139       149       159       169     
                             1-MSE                                                                                                            116-MSE
   Legend:   → Mismatch (orange background)
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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 2OU5)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: FMN-binding (25)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q28VU1_JANSC | Q28VU1)
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: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.
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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