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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE PUTATIVE NAD(P)H-FLAVIN OXIDOREDUCTASE FROM STREPTOCOCCUS PYOGENES M1 GAS
 
Authors :  Y. Kim, E. Duggan, S. Clancy, A. Joachimiak, Midwest Center For Stru Genomics (Mcsg)
Date :  13 Jun 06  (Deposition) - 04 Jul 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Alpha-Beta Structure, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, E. Duggan, S. Clancy, A. Joachimiak
The Crystal Structure Of The Putative Nad(P)H-Flavin Oxidoreductase From Streptococcus Pyogenes M1 Gas
To Be Published 2006
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE NAD(P)H-FLAVIN OXIDOREDUCTASE
    Chains: A, B, C, D
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PUTATIVE NAD(P)H-FLAVIN OXIDOREDUCTASE
    Organism Scientific: STREPTOCOCCUS PYOGENES SEROTYPE M1
    Organism Taxid: 301447
    Strain: SF370
    Synonym: NADP, H-DEPENDENT QUINONE REDUCTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 39)

Asymmetric Unit (3, 39)
No.NameCountTypeFull Name
1FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
2MSE30Mod. Amino AcidSELENOMETHIONINE
3SO45Ligand/IonSULFATE ION
Biological Unit 1 (3, 20)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2MSE15Mod. Amino AcidSELENOMETHIONINE
3SO43Ligand/IonSULFATE ION
Biological Unit 2 (3, 19)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2MSE15Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:89 , HIS A:90 , HOH A:892BINDING SITE FOR RESIDUE SO4 A 801
2AC2SOFTWAREARG A:20 , TRP A:70 , FMN A:702 , ARG B:105 , ARG B:116 , TYR B:120BINDING SITE FOR RESIDUE SO4 B 802
3AC3SOFTWAREARG B:202 , PRO B:204 , LYS B:205 , HIS B:206BINDING SITE FOR RESIDUE SO4 B 803
4AC4SOFTWAREARG C:135 , PHE C:138 , ASP C:139 , TYR C:171 , HOH C:717 , MSE D:128BINDING SITE FOR RESIDUE SO4 D 804
5AC5SOFTWAREARG A:202 , HOH A:939 , LYS D:23 , GLU D:24 , GLU D:25BINDING SITE FOR RESIDUE SO4 D 805
6AC6SOFTWAREPRO A:43 , SER A:44 , SER A:45 , ARG A:105 , GLN A:144 , ILE A:147 , HOH A:806 , ARG B:16 , THR B:17 , ALA B:18 , GLY B:71 , PRO B:165 , ILE B:166 , GLU B:167 , GLY B:168 , GLN B:208 , ARG B:210 , HOH B:871 , HOH B:947BINDING SITE FOR RESIDUE FMN B 701
7AC7SOFTWAREARG A:16 , THR A:17 , ALA A:18 , ARG A:20 , GLY A:71 , GLN A:75 , TYR A:146 , CYS A:164 , PRO A:165 , ILE A:166 , GLU A:167 , GLY A:168 , ARG A:210 , HOH A:824 , HOH A:875 , HOH A:915 , HOH A:941 , HOH A:943 , PRO B:43 , SER B:44 , SER B:45 , GLN B:144 , ILE B:147 , SO4 B:802 , HOH B:890BINDING SITE FOR RESIDUE FMN A 702
8AC8SOFTWAREPRO C:43 , SER C:44 , SER C:45 , GLN C:144 , ILE C:147 , HOH C:712 , ARG D:16 , THR D:17 , ALA D:18 , GLY D:71 , GLN D:75 , TYR D:146 , CYS D:164 , PRO D:165 , ILE D:166 , GLU D:167 , GLY D:168 , ARG D:210 , HOH D:880 , HOH D:886 , HOH D:907BINDING SITE FOR RESIDUE FMN D 703
9AC9SOFTWAREARG C:16 , THR C:17 , ALA C:18 , ARG C:20 , GLY C:71 , GLN C:75 , TYR C:146 , CYS C:164 , PRO C:165 , ILE C:166 , GLU C:167 , GLY C:168 , ARG C:210 , HOH C:828 , PRO D:43 , SER D:44 , SER D:45 , GLN D:144 , ILE D:147BINDING SITE FOR RESIDUE FMN C 704

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HAY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2HAY)

(-) Sequences/Alignments

Asymmetric 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:217
 aligned with Q9A120_STRP1 | Q9A120 from UniProtKB/TrEMBL  Length:221

    Alignment length:217
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       
         Q9A120_STRP1     5 IHHQIQQALHFRTAVRVYKEEKISDEDLALILDAAWLSPSSIGLEGWRFVVLDNKPIKEEIKPFAWGAQYQLETASHFILLIAEKHARYDSPAIKNSLLRRGIKEGDGLNSRLKLYESFQKEDMDMADNPRALFDWTAKQTYIALGNMMMTAALLGIDTCPIEGFHYDKVNHILAKHNVIDLEKEGIASMLSLGYRLRDPKHAQVRKPKEEVISVVK 221
               SCOP domains d2haya_ A: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains 2hayA00 A:5-221 NADH Oxidase                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...........hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhh..hhhhhhhh.eeeeeeee......hhhhhhhhhhh......hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh.......eeeeeeeeee.............hhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hay A   5 IHHQIQQALHFRTAVRVYKEEKISDEDLALILDAAWLSPSSIGLEGWRFVVLDNKPIKEEIKPFAWGAQYQLETASHFILLIAEKHARYDSPAIKNSLLRRGIKEGDGLNSRLKLYESFQKEDmDmADNPRALFDWTAKQTYIALGNmmmTAALLGIDTCPIEGFHYDKVNHILAKHNVIDLEKEGIASmLSLGYRLRDPKHAQVRKPKEEVmSVVK 221
                                    14        24        34        44        54        64        74        84        94       104       114       124   | | 134       144       154       164       174       184       194       204       214  |    
                                                                                                                                                     128-MSE                 152-MSE                                   194-MSE                217-MSE
                                                                                                                                                       130-MSE                153-MSE                                                                
                                                                                                                                                                               154-MSE                                                               


Chain B from PDB  Type:PROTEIN  Length:221
 aligned with Q9A120_STRP1 | Q9A120 from UniProtKB/TrEMBL  Length:221

    Alignment length:221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 
         Q9A120_STRP1     1 MDQTIHHQIQQALHFRTAVRVYKEEKISDEDLALILDAAWLSPSSIGLEGWRFVVLDNKPIKEEIKPFAWGAQYQLETASHFILLIAEKHARYDSPAIKNSLLRRGIKEGDGLNSRLKLYESFQKEDMDMADNPRALFDWTAKQTYIALGNMMMTAALLGIDTCPIEGFHYDKVNHILAKHNVIDLEKEGIASMLSLGYRLRDPKHAQVRKPKEEVISVVK 221
               SCOP domains d2hayb_ B: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains -2hayB00 B:2-221 NADH Oxidase                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhh..hhhhhhhh.eeeeeeee......hhhhhhhhhh.......hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhh.......eeeeeeeeee.............hhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hay B   1 mDQTIHHQIQQALHFRTAVRVYKEEKISDEDLALILDAAWLSPSSIGLEGWRFVVLDNKPIKEEIKPFAWGAQYQLETASHFILLIAEKHARYDSPAIKNSLLRRGIKEGDGLNSRLKLYESFQKEDmDmADNPRALFDWTAKQTYIALGNmmmTAALLGIDTCPIEGFHYDKVNHILAKHNVIDLEKEGIASmLSLGYRLRDPKHAQVRKPKEEVmSVVK 221
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 |||   160       170       180       190   |   200       210      |220 
                            |                                                                                                                            128-MSE                 152-MSE                                   194-MSE                217-MSE
                            1-MSE                                                                                                                          130-MSE                153-MSE                                                                
                                                                                                                                                                                   154-MSE                                                               


Chain C from PDB  Type:PROTEIN  Length:216
 aligned with Q9A120_STRP1 | Q9A120 from UniProtKB/TrEMBL  Length:221

    Alignment length:218
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213        
         Q9A120_STRP1     4 TIHHQIQQALHFRTAVRVYKEEKISDEDLALILDAAWLSPSSIGLEGWRFVVLDNKPIKEEIKPFAWGAQYQLETASHFILLIAEKHARYDSPAIKNSLLRRGIKEGDGLNSRLKLYESFQKEDMDMADNPRALFDWTAKQTYIALGNMMMTAALLGIDTCPIEGFHYDKVNHILAKHNVIDLEKEGIASMLSLGYRLRDPKHAQVRKPKEEVISVVK 221
               SCOP domains d2hayc_ C: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains 2hayC00 C:4-221 NADH Oxidase                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...........hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhh..hhhhhhhh.eeeeeeee......hhhhhhhhhhh.....hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh.......eeeeeeeeee......--.....hhhh.eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hay C   4 TIHHQIQQALHFRTAVRVYKEEKISDEDLALILDAAWLSPSSIGLEGWRFVVLDNKPIKEEIKPFAWGAQYQLETASHFILLIAEKHARYDSPAIKNSLLRRGIKEGDGLNSRLKLYESFQKEDmDmADNPRALFDWTAKQTYIALGNmmmTAALLGIDTCPIEGFHYDKVNHILAKHNVIDLEKEGIASmLSLGYRLRDP--AQVRKPKEEVmSVVK 221
                                    13        23        33        43        53        63        73        83        93       103       113       123    | |133       143       153|      163       173       183       193|      203|  |   213   |    
                                                                                                                                                      128-MSE                 152-MSE                                   194-MSE   204  |       217-MSE
                                                                                                                                                        130-MSE                153-MSE                                               207              
                                                                                                                                                                                154-MSE                                                               


Chain D from PDB  Type:PROTEIN  Length:222
 aligned with Q9A120_STRP1 | Q9A120 from UniProtKB/TrEMBL  Length:221

    Alignment length:222
                             1                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219  
         Q9A120_STRP1     - -MDQTIHHQIQQALHFRTAVRVYKEEKISDEDLALILDAAWLSPSSIGLEGWRFVVLDNKPIKEEIKPFAWGAQYQLETASHFILLIAEKHARYDSPAIKNSLLRRGIKEGDGLNSRLKLYESFQKEDMDMADNPRALFDWTAKQTYIALGNMMMTAALLGIDTCPIEGFHYDKVNHILAKHNVIDLEKEGIASMLSLGYRLRDPKHAQVRKPKEEVISVVK 221
               SCOP domains d2hayd_ D: automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains 2hayD00 D:0-221 NADH Oxidase                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhh..hhhhhhhh.eeeeeeee......hhhhhhhhhhh......hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh.......eeeeeeeeee.............hhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2hay D   0 AmDQTIHHQIQQALHFRTAVRVYKEEKISDEDLALILDAAWLSPSSIGLEGWRFVVLDNKPIKEEIKPFAWGAQYQLETASHFILLIAEKHARYDSPAIKNSLLRRGIKEGDGLNSRLKLYESFQKEDmDmADNPRALFDWTAKQTYIALGNmmmTAALLGIDTCPIEGFHYDKVNHILAKHNVIDLEKEGIASmLSLGYRLRDPKHAQVRKPKEEVmSVVK 221
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129|      139       149  |||  159       169       179       189    |  199       209       219  
                             1-MSE                                                                                                                        128-MSE                 152-MSE                                   194-MSE                217-MSE
                                                                                                                                                            130-MSE                153-MSE                                                                
                                                                                                                                                                                    154-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9A120_STRP1 | Q9A120)
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.
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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  2hay
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