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(-) Description

Title :  CRYSTAL STRUCTURE OF A PYRIDOXAMINE 5'-PHOSPHATE OXIDASE-RELATED, FMN BINDING PROTEIN (NPUN_F5749) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.40 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  23 Aug 06  (Deposition) - 05 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pyridoxamine 5'-Phosphate Oxidase-Related Protein, 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 Uncharacterized Conserved Protein Of Cog5135 (Zp_00109616. 1) From Nostoc Punctiforme Pcc 73102 A 1. 40 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED CONSERVED PROTEIN OF COG5135
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ZP_00109616.1
    Organism Scientific: NOSTOC PUNCTIFORME
    Organism Taxid: 63737
    Strain: PCC 73102

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 29)

Asymmetric/Biological Unit (4, 29)
No.NameCountTypeFull Name
1EDO20Ligand/Ion1,2-ETHANEDIOL
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3GOL1Ligand/IonGLYCEROL
4MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:25 , ARG A:40 , THR A:41 , LEU A:42 , VAL A:43 , ARG A:45 , ILE A:57 , THR A:58 , SER A:62 , ALA A:63 , LYS A:64 , EDO A:306 , EDO A:307 , HOH A:313 , HOH A:341 , HOH A:342 , HOH A:374 , HOH A:481 , TYR B:79 , GLN B:86 , ARG B:88 , EDO B:305 , HOH B:320BINDING SITE FOR RESIDUE FMN A 300
02AC2SOFTWARETYR A:79 , GLN A:86 , ARG A:88 , HOH A:394 , TYR B:25 , ARG B:40 , THR B:41 , LEU B:42 , VAL B:43 , ILE B:57 , THR B:58 , SER B:62 , ALA B:63 , LYS B:64 , EDO B:301 , EDO B:302 , EDO B:306 , HOH B:314 , HOH B:343 , HOH B:347 , HOH B:477 , HOH B:478BINDING SITE FOR RESIDUE FMN B 300
03AC3SOFTWAREGLN A:174 , GLN B:123 , FMN B:300 , EDO B:302 , HOH B:456BINDING SITE FOR RESIDUE EDO B 301
04AC4SOFTWAREGLN B:123 , PHE B:124 , FMN B:300 , EDO B:301 , HOH B:391BINDING SITE FOR RESIDUE EDO B 302
05AC5SOFTWAREASN A:82 , ARG A:170 , HOH A:369 , HOH A:467 , ASP B:146 , HOH B:322BINDING SITE FOR RESIDUE EDO A 301
06AC6SOFTWAREALA A:111 , GLN A:114 , GLU A:115 , GOL B:309BINDING SITE FOR RESIDUE EDO A 302
07AC7SOFTWAREGLN A:32 , HOH A:321 , GLU B:75 , ARG B:88 , EDO B:304 , HOH B:333 , HOH B:353BINDING SITE FOR RESIDUE EDO B 303
08AC8SOFTWAREGLU B:75 , ARG B:88 , MSE B:89 , ALA B:90 , GLN B:163 , ASP B:165 , LEU B:178 , EDO B:303 , HOH B:422BINDING SITE FOR RESIDUE EDO B 304
09AC9SOFTWAREMSE A:1 , LEU A:3 , ASP A:50 , THR A:51BINDING SITE FOR RESIDUE EDO A 303
10BC1SOFTWARESER A:62 , ALA A:63 , PRO A:129 , GLY A:130 , FMN A:300 , ARG B:176 , HOH B:451BINDING SITE FOR RESIDUE EDO B 305
11BC2SOFTWAREGLU A:75 , ARG A:88 , ALA A:90 , GLN A:163 , ASP A:165 , HOH A:390BINDING SITE FOR RESIDUE EDO A 304
12BC3SOFTWAREMSE A:1 , ASN A:52 , ARG A:181 , GLN A:185 , HOH A:349 , HOH A:368BINDING SITE FOR RESIDUE EDO A 305
13BC4SOFTWAREILE A:57 , GLN A:123 , PHE A:124 , FMN A:300 , HOH A:354 , HOH A:401 , HOH A:481BINDING SITE FOR RESIDUE EDO A 306
14BC5SOFTWAREGLN A:123 , FMN A:300 , HOH A:482 , GLN B:174 , HOH B:365BINDING SITE FOR RESIDUE EDO A 307
15BC6SOFTWAREASP A:100 , SER A:101 , HIS A:102 , GLN A:103 , ASP A:104 , HOH A:459BINDING SITE FOR RESIDUE EDO A 308
16BC7SOFTWAREPRO A:72 , LEU A:93 , THR A:94 , LEU A:95 , HIS A:102 , HOH A:426 , HOH A:474BINDING SITE FOR RESIDUE EDO A 309
17BC8SOFTWAREARG A:176 , HOH A:457 , SER B:62 , ALA B:63 , PRO B:129 , GLY B:130 , FMN B:300 , HOH B:488BINDING SITE FOR RESIDUE EDO B 306
18BC9SOFTWARESER A:98 , ASP A:99 , GLN A:103 , ARG B:121 , HOH B:312 , HOH B:450BINDING SITE FOR RESIDUE EDO A 310
19CC1SOFTWAREMSE B:1 , LEU B:3 , ASP B:50 , THR B:51 , ASN B:52 , HOH B:328BINDING SITE FOR RESIDUE EDO B 307
20CC2SOFTWAREASN B:34 , HOH B:481BINDING SITE FOR RESIDUE EDO B 308
21CC3SOFTWARETHR A:60 , ARG A:61 , SER A:62 , ALA A:63 , ALA A:65 , ASP A:66BINDING SITE FOR RESIDUE EDO A 311
22CC4SOFTWAREGLU A:75 , ARG A:88 , HOH A:488 , GLN B:32 , ALA B:38 , HOH B:330BINDING SITE FOR RESIDUE EDO A 312
23CC5SOFTWAREPRO A:107 , GLN A:114 , EDO A:302 , GLN B:114 , HOH B:334 , HOH B:447BINDING SITE FOR RESIDUE GOL B 309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I51)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:172 -Pro A:173
2Glu B:172 -Pro B:173

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I51)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2I51)

(-) Exons   (0, 0)

(no "Exon" information available for 2I51)

(-) 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:194
 aligned with B2J933_NOSP7 | B2J933 from UniProtKB/TrEMBL  Length:194

    Alignment length:194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    
         B2J933_NOSP7     1 MSLAPWRGAIAHALHRNRSLVYARYLQLATVQPNGRPANRTLVFRGFLEDTNQLRFITDTRSAKADQIQQQPWAEICWYFPNTREQFRMAGDLTLISSDDSHQDLQPARIAMWQELSDAARLQFGWPYPGKPRIKESGAFEPSPPDPIEPVPNFCLLLLDPVQVDHLELRGEPQNRWLYHRNDQQEWSSEAINP 194
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2i51A00 A:2-194 Electron Transport, Fmn-binding Protein; Chain A                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh..hhhh.eeeeeee.....eeeeeee..........eeeeee..hhhhhhhhhh.eeeeeeee....eeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh............eeeeeeeeeeeeeee......eeeeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i51 A   1 mSLAPWRGAIAHALHRNRSLVYARYLQLATVQPNGRPANRTLVFRGFLEDTNQLRFITDTRSAKADQIQQQPWAEICWYFPNTREQFRmAGDLTLISSDDSHQDLQPARIAmWQELSDAARLQFGWPYPGKPRIKESGAFEPSPPDPIEPVPNFCLLLLDPVQVDHLELRGEPQNRWLYHRNDQQEWSSEAINP 194
                            |       10        20        30        40        50        60        70        80        90       100       110 |     120       130       140       150       160       170       180       190    
                            |                                                                                      89-MSE                112-MSE                                                                              
                            1-MSE                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:191
 aligned with B2J933_NOSP7 | B2J933 from UniProtKB/TrEMBL  Length:194

    Alignment length:195
                             1                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189     
         B2J933_NOSP7     - -MSLAPWRGAIAHALHRNRSLVYARYLQLATVQPNGRPANRTLVFRGFLEDTNQLRFITDTRSAKADQIQQQPWAEICWYFPNTREQFRMAGDLTLISSDDSHQDLQPARIAMWQELSDAARLQFGWPYPGKPRIKESGAFEPSPPDPIEPVPNFCLLLLDPVQVDHLELRGEPQNRWLYHRNDQQEWSSEAINP 194
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2i51B00 B:0-194 Electron Transport, Fmn-binding Protein; Chain A                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh..hhhh.eeeeeee.....eeeeeee..........eeeeee..hhhhhhhhhh.eeeeeeee....eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......----................eeeeeeeeeeeeeee......eeeeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i51 B   0 GmSLAPWRGAIAHALHRNRSLVYARYLQLATVQPNGRPANRTLVFRGFLEDTNQLRFITDTRSAKADQIQQQPWAEICWYFPNTREQFRmAGDLTLISSDDSHQDLQPARIAmWQELSDAARLQFGWPYPGKPR----GAFEPSPPDPIEPVPNFCLLLLDPVQVDHLELRGEPQNRWLYHRNDQQEWSSEAINP 194
                             |       9        19        29        39        49        59        69        79        89        99       109  |    119       129   |   139       149       159       169       179       189     
                             1-MSE                                                                                  89-MSE                112-MSE              133  138                                                        


Chain B from PDB  Type:PROTEIN  Length:191
 aligned with Q8YQ04_NOSS1 | Q8YQ04 from UniProtKB/TrEMBL  Length:194

    Alignment length:195
                             1                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189     
         Q8YQ04_NOSS1     - -MSLAPWRSAIAHALHCNRSLVYSHYLQLATVKANGHPANRTIVFRGFLADTNQLKFITDARSEKIDQIQHQPWAEACWYFPNTREQFRITGQLTLVASDESHPHLQPARISTWQELSDAARLQFAWPHPSQPRGEDQAAFNPPPPNPQQPIPNFCLLLLEPTQIDHLELRGEPQNRYLYRRDHNQEWTIQGVNP 194
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2i51B00 B:0-194 Electron Transport, Fmn-binding Protein; Chain A                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh..hhhh.eeeeeee.....eeeeeee..........eeeeee..hhhhhhhhhh.eeeeeeee....eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......----................eeeeeeeeeeeeeee......eeeeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i51 B   0 GmSLAPWRGAIAHALHRNRSLVYARYLQLATVQPNGRPANRTLVFRGFLEDTNQLRFITDTRSAKADQIQQQPWAEICWYFPNTREQFRmAGDLTLISSDDSHQDLQPARIAmWQELSDAARLQFGWPYPGKPR----GAFEPSPPDPIEPVPNFCLLLLDPVQVDHLELRGEPQNRWLYHRNDQQEWSSEAINP 194
                             |       9        19        29        39        49        59        69        79        89        99       109  |    119       129   |   139       149       159       169       179       189     
                             1-MSE                                                                                  89-MSE                112-MSE              133  138
   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 2I51)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I51)

(-) Gene Ontology  (4, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (B2J933_NOSP7 | B2J933)
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.

Chain B   (Q8YQ04_NOSS1 | Q8YQ04)
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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