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(-) Description

Title :  CRYSTAL STRUCTURE OF A PYRIDINE NUCLEOTIDE-DISULFIDE FAMILY OXIDOREDUCTASE FROM THE ENTEROCOCCUS FAECALIS V583
 
Authors :  D. Kumaran, K. Baumann, S. K. Burley, S. Swaminathan, New York Sgx Re Center For Structural Genomics (Nysgxrc)
Date :  09 Aug 10  (Deposition) - 06 Oct 10  (Release) - 06 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Oxidoreductase, Coa-Disulfide Reductase, Rossmann-Fold, Nad(P)(+)- Binding Protein, Psi Ii (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Kumaran, K. Baumann, S. K. Burley, S. Swaminathan
Crystal Structure Of A Pyridine Nucleotide-Disulfide Family Oxidoreductase From The Enterococcus Faecalis V583
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OXIDOREDUCTASE, PYRIDINE NUCLEOTIDE-DISULFIDE FAMILY
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: EF1932, EF_1932
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 1351

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric/Biological Unit (3, 18)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MSE14Mod. Amino AcidSELENOMETHIONINE
3NA2Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:7 , SER A:9 , PHE A:10 , ALA A:11 , ASP A:32 , LYS A:33 , GLN A:34 , ARG A:77 , VAL A:79 , ALA A:108 , THR A:109 , GLY A:110 , LYS A:130 , GLU A:159 , TYR A:246 , GLY A:276 , ASP A:277 , PRO A:293 , LEU A:294 , VAL A:295 , ALA A:298 , HOH A:459 , HOH A:527 , HOH A:538 , HOH A:539 , TYR B:418 , PRO B:420 , HOH B:456BINDING SITE FOR RESIDUE FAD A 500
2AC2SOFTWAREGLY A:342 , PHE A:345 , GLN A:347 , HOH A:540 , HOH A:541BINDING SITE FOR RESIDUE NA A 501
3AC3SOFTWARETYR A:418 , GLY B:7 , SER B:9 , PHE B:10 , ALA B:11 , ASP B:32 , LYS B:33 , GLN B:34 , ARG B:77 , VAL B:79 , THR B:109 , GLY B:110 , ALA B:111 , LYS B:130 , GLU B:159 , TYR B:246 , GLY B:276 , ASP B:277 , PRO B:293 , LEU B:294 , VAL B:295 , ALA B:298 , HOH B:470 , HOH B:482 , HOH B:546BINDING SITE FOR RESIDUE FAD B 500
4AC4SOFTWAREGLY B:342 , PHE B:345 , GLN B:347 , HOH B:547BINDING SITE FOR RESIDUE NA B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OC4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro B:359 -Pro B:360

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OC4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OC4)

(-) Exons   (0, 0)

(no "Exon" information available for 3OC4)

(-) 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:422
 aligned with Q833L5_ENTFA | Q833L5 from UniProtKB/TrEMBL  Length:444

    Alignment length:442
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440  
         Q833L5_ENTFA     1 MKIVIIGASFAGISAAIASRKKYPQAEISLIDKQATVGYLSGGLSAYFNHTINELHEARYITEEELRRQKIQLLLNREVVAMDVENQLIAWTRKEEQQWYSYDKLILATGASQFSTQIRGSQTEKLLKYKFLSGALAAVPLLENSQTVAVIGAGPIGMEAIDFLVKMKKTVHVFESLENLLPKYFDKEMVAEVQKSLEKQAVIFHFEETVLGIEETANGIVLETSEQEISCDSGIFALNLHPQLAYLDKKIQRNLDQTIAVDAYLQTSVPNVFAIGDCISVMNEPVAETFYAPLVNNAVRTGLVVANNLEEKTHRFIGSLRTMGTKVGDYYLASTGLTETEGLFFPQTLASIIVRQPAPPLQHGTEILGKLIYDKVTQRVLGAQLCSKNNCLEKINTLALSIQTGQTLTDLLQKDYFYQPSLTNIYDITNLMGASAYWREND 442
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh...eeeee...........----------------...hhhhhhhh.eeee...eeeeee....eeeeee..eeeeee..eeee..................eee.hhh.----.hhhhhh..eeeee..hhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhhhh..eeeee...eeeeee....eeeee...eeee.eeee...................................eee.hhhh.eeehhhheee...hhhhhhhhhhhhh................eeeee..eeeeeee..hhhhhhh...eeeeeeeee........eeeeeeeee.....eeeeeeee....hhhhhhhhhhhhh..hhhhhhh.............hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oc4 A  -1 LKIVIIGASFAGISAAIASRKKYPQAEISLIDKQATVGYLSG----------------RYITEEELRRQKIQLLLNREVVAmDVENQLIAWTRKEEQQWYSYDKLILATGASQFSTQIRGSQTEKLLKYKFLS----AVPLLENSQTVAVIGAGPIGmEAIDFLVKmKKTVHVFESLENLLPKYFDKEmVAEVQKSLEKQAVIFHFEETVLGIEETANGIVLETSEQEISCDSGIFALNLHPQLAYLDKKIQRNLDQTIAVDAYLQTSVPNVFAIGDCISVmNEPVAETFYAPLVNNAVRTGLVVANNLEEKTHRFIGSLRTmGTKVGDYYLASTGLTETEGLFFPQTLASIIVRQPAPPLQHGTEILGKLIYDKVTQRVLGAQLCSKNNCLEKINTLALSIQTGQTLTDLLQKDYFYQPSLTNIYDITNLmGASAYWREND 442
                            ||      10        20        30        40 |       -        60        70        80 |      90       100       110       120       130  |    140       150       160      |170       180       190       200       210       220       230       240       250       260       270       280 |     290       300       310       320  |    330       340       350       360       370       380       390       400       410       420       430 |     440  
                            ||                                      42               59                     82-MSE                                            133  138                 158-MSE  167-MSE               189-MSE                                                                                      282-MSE                                  323-MSE                                                                                                      432-MSE      
                           -1|                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                             2                                                                                                                                                                                                                                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:421
 aligned with Q833L5_ENTFA | Q833L5 from UniProtKB/TrEMBL  Length:444

    Alignment length:444
                             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    
         Q833L5_ENTFA     - -MKIVIIGASFAGISAAIASRKKYPQAEISLIDKQATVGYLSGGLSAYFNHTINELHEARYITEEELRRQKIQLLLNREVVAMDVENQLIAWTRKEEQQWYSYDKLILATGASQFSTQIRGSQTEKLLKYKFLSGALAAVPLLENSQTVAVIGAGPIGMEAIDFLVKMKKTVHVFESLENLLPKYFDKEMVAEVQKSLEKQAVIFHFEETVLGIEETANGIVLETSEQEISCDSGIFALNLHPQLAYLDKKIQRNLDQTIAVDAYLQTSVPNVFAIGDCISVMNEPVAETFYAPLVNNAVRTGLVVANNLEEKTHRFIGSLRTMGTKVGDYYLASTGLTETEGLFFPQTLASIIVRQPAPPLQHGTEILGKLIYDKVTQRVLGAQLCSKNNCLEKINTLALSIQTGQTLTDLLQKDYFYQPSLTNIYDITNLMGASAYWRENDE 443
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------------------------------------------               --------------------------------------------------------------------------      ---------Pyr_redox-3oc4B01 B:147-229                                                        --------------------------------------------------------------------------------------------Pyr_redox_dim-3oc4B05 B:322-428                                                                            --------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------               --------------------------------------------------------------------------      ---------Pyr_redox-3oc4B02 B:147-229                                                        --------------------------------------------------------------------------------------------Pyr_redox_dim-3oc4B06 B:322-428                                                                            --------------- Pfam domains (2)
           Pfam domains (3) --Pyr_redox_2-3oc4B03 B:2-283                                                                                                                                                                                                                                                               -----------------------------------------------------------------------------  --------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --Pyr_redox_2-3oc4B04 B:2-283                                                                                                                                                                                                                                                               -----------------------------------------------------------------------------  --------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh...eeeee...........---------------....hhhhhhhh..eee...eeeeee....eeeee....eeeee..eeee..................eee...------.hhhhhh..eeeee..hhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhhhh..eeeee...eeeeeee..eeeeee...eeee.eeee...................................eee.hhhh.eeehhhheee...hhhhhhhhhhhhh................eeeee..eeeeeee.hhhhhh.....eeeeeeeee...--...eeeeeeeee.....eeeeeeee....hhhhhhhhhhhhh..hhhhhhh.............hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oc4 B  -2 SLKIVIIGASFAGISAAIASRKKYPQAEISLIDKQATVGYLSG---------------ARYITEEELRRQKIQLLLNREVVAmDVENQLIAWTRKEEQQWYSYDKLILATGASQFSTQIRGSQTEKLLKYKF------AVPLLENSQTVAVIGAGPIGmEAIDFLVKmKKTVHVFESLENLLPKYFDKEmVAEVQKSLEKQAVIFHFEETVLGIEETANGIVLETSEQEISCDSGIFALNLHPQLAYLDKKIQRNLDQTIAVDAYLQTSVPNVFAIGDCISVmNEPVAETFYAPLVNNAVRTGLVVANNLEEKTHRFIGSLRTmGTKVGDYYLASTGLTETEGLFFPQTLASIIVRQPAPP--HGTEILGKLIYDKVTQRVLGAQLCSKNNCLEKINTLALSIQTGQTLTDLLQKDYFYQPSLTNIYDITNLmGASAYWRENDE 443
                             ||      9        19        29        39  |      -        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    
                            -1|                                      42              58                      82-MSE                                          131    138                 158-MSE  167-MSE               189-MSE                                                                                      282-MSE                                  323-MSE                              360  |                                                                  432-MSE       
                              2                                                                                                                                                                                                                                                                                                                                                                      363
   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 3OC4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OC4)

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: Pyr_redox_dim] (44)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q833L5_ENTFA | Q833L5)
molecular function
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    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.
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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