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(-) Description

Title :  CRYSTAL STRUCTURE OF SMU.1420 FROM STREPTOCOCCUS MUTANS UA159
 
Authors :  Z. X. Wang, X. -D. Su
Date :  11 Jan 10  (Deposition) - 12 Jan 11  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Nadph:Quinone Oxidoreductase, Mdab, Smu. 1420, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. X. Wang, L. Li, Y. H. Dong, X. -D. Su
Structural And Biochemical Characterization Of Mdab From Cariogenic Streptococcus Mutans Reveals An Nadph-Specific Quinone Oxidoreductase
Acta Crystallogr. , Sect. D V. 70 912 2014
PubMed-ID: 24699637  |  Reference-DOI: 10.1107/S1399004713033749

(-) Compounds

Molecule 1 - PUTATIVE OXIDOREDUCTASE
    Chains: A, B, C, D
    EC Number: 1.6.99.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SMU.1420
    Organism Scientific: STREPTOCOCCUS MUTANS
    Organism Taxid: 210007
    Strain: UA159
    Synonym: SMU.1420

 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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:9 , SER A:14 , PHE A:15 , ASN A:16 , PRO A:82 , ILE A:83 , TRP A:84 , TRP A:85 , SER A:86 , THR A:127 , HIS A:128 , ASN A:129 , THR A:130 , TYR A:141 , ARG A:174 , HOH A:222 , HOH A:228 , HOH A:340 , LEU B:47 , ARG B:55 , NAP B:198 , HOH B:236BINDING SITE FOR RESIDUE FAD A 197
2AC2SOFTWAREARG A:55 , TYR A:106 , TYR A:108 , HOH A:225 , TRP B:85 , FAD B:197BINDING SITE FOR RESIDUE NAP A 198
3AC3SOFTWARELEU A:47 , ARG A:55 , NAP A:198 , HOH A:219 , HIS B:9 , SER B:14 , PHE B:15 , ASN B:16 , PRO B:82 , ILE B:83 , TRP B:84 , TRP B:85 , SER B:86 , THR B:127 , HIS B:128 , ASN B:129 , THR B:130 , TYR B:141 , GLU B:167 , ARG B:174 , GLN B:175 , HOH B:213 , HOH B:224 , HOH B:226 , HOH B:239 , HOH B:259 , HOH B:274 , HOH B:282 , HOH B:355BINDING SITE FOR RESIDUE FAD B 197
4AC4SOFTWARETRP A:85 , ASN A:129 , FAD A:197 , ARG B:55 , TYR B:106 , TYR B:108BINDING SITE FOR RESIDUE NAP B 198
5AC5SOFTWAREHIS C:9 , SER C:14 , PHE C:15 , ASN C:16 , ILE C:83 , TRP C:84 , TRP C:85 , SER C:86 , THR C:127 , HIS C:128 , ASN C:129 , THR C:130 , TYR C:141 , GLU C:167 , ARG C:174 , GLN C:175 , NAP C:198 , HOH C:229 , HOH C:236 , HOH C:237 , HOH C:307 , ARG D:55 , HOH D:201BINDING SITE FOR RESIDUE FAD C 197
6AC6SOFTWARETRP C:85 , THR C:130 , ALA C:134 , TYR C:141 , FAD C:197 , ARG D:55 , TYR D:106 , TYR D:108 , GLN D:148 , PRO D:152BINDING SITE FOR RESIDUE NAP C 198
7AC7SOFTWARETYR C:106 , TYR C:108 , FAD D:197BINDING SITE FOR RESIDUE NAP C 199
8AC8SOFTWARELEU C:47 , ARG C:55 , NAP C:199 , HIS D:9 , SER D:14 , PHE D:15 , ASN D:16 , GLU D:18 , PRO D:82 , ILE D:83 , TRP D:84 , TRP D:85 , SER D:86 , THR D:127 , HIS D:128 , ASN D:129 , THR D:130 , TYR D:141 , ASP D:171 , ARG D:174 , GLN D:175 , HOH D:202 , HOH D:216 , HOH D:230 , HOH D:236 , HOH D:247BINDING SITE FOR RESIDUE FAD D 197

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:156 -Pro A:157
2Ser B:156 -Pro B:157
3Ser C:156 -Pro C:157
4Ser D:156 -Pro D:157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LCM)

(-) 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:196
 aligned with Q8DTD1_STRMU | Q8DTD1 from UniProtKB/TrEMBL  Length:188

    Alignment length:196
                                                                                                                                                                                                                     188        
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       | -      
         Q8DTD1_STRMU     1 MKILIVYTHPNPTSFNAEILKQVQTNLSKEHTVSTLDLYAEHFDPVLQFNETHKRRDLAKVAEMEKYRDLVTWADHLIFIFPIWWSGMPAILKGFIDRVFVADFAYSYKKVGLEGHLQGKSAWIITTHNTPSFAMPFVQDYGKVLKKQILKPCAISPVKLTELTSIEKISDDERQKLLHKVAQITRNI--------   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhh....eeeeee................hhhhhhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhh.....eee....eee.....eeeeeee...hhhhh......hhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lcm A   1 MKILIVYTHPNPTSFNAEILKQVQTNLSKEHTVSTLDLYAEHFDPVLQFNETHKRRDLAKVAEMEKYRDLVTWADHLIFIFPIWWSGMPAILKGFIDRVFVADFAYSYKKVGLEGHLQGKSAWIITTHNTPSFAMPFVQDYGKVLKKQILKPCAISPVKLTELTSIEKISDDERQKLLHKVAQITRNILEHHHHHH 196
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190      


Chain B from PDB  Type:PROTEIN  Length:188
 aligned with Q8DTD1_STRMU | Q8DTD1 from UniProtKB/TrEMBL  Length:188

    Alignment length:188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
         Q8DTD1_STRMU     1 MKILIVYTHPNPTSFNAEILKQVQTNLSKEHTVSTLDLYAEHFDPVLQFNETHKRRDLAKVAEMEKYRDLVTWADHLIFIFPIWWSGMPAILKGFIDRVFVADFAYSYKKVGLEGHLQGKSAWIITTHNTPSFAMPFVQDYGKVLKKQILKPCAISPVKLTELTSIEKISDDERQKLLHKVAQITRNI 188
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhh....eeeeee................hhhhhhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhh.....eee....eee.....eeeeeee...hhhhhhhh...hhhhhhhh........eeeeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lcm B   1 MKILIVYTHPNPTSFNAEILKQVQTNLSKEHTVSTLDLYAEHFDPVLQFNETHKRRDLAKVAEMEKYRDLVTWADHLIFIFPIWWSGMPAILKGFIDRVFVADFAYSYKKVGLEGHLQGKSAWIITTHNTPSFAMPFVQDYGKVLKKQILKPCAISPVKLTELTSIEKISDDERQKLLHKVAQITRNI 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        


Chain C from PDB  Type:PROTEIN  Length:196
 aligned with Q8DTD1_STRMU | Q8DTD1 from UniProtKB/TrEMBL  Length:188

    Alignment length:196
                                                                                                                                                                                                                     188        
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       | -      
         Q8DTD1_STRMU     1 MKILIVYTHPNPTSFNAEILKQVQTNLSKEHTVSTLDLYAEHFDPVLQFNETHKRRDLAKVAEMEKYRDLVTWADHLIFIFPIWWSGMPAILKGFIDRVFVADFAYSYKKVGLEGHLQGKSAWIITTHNTPSFAMPFVQDYGKVLKKQILKPCAISPVKLTELTSIEKISDDERQKLLHKVAQITRNI--------   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhh....eeeeeehhhhh...........hhhhhhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhh.....eee....eee.....eeeeeee...hhhhhhhh...hhhhhhh.hhhhh...eeeeee......hhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lcm C   1 MKILIVYTHPNPTSFNAEILKQVQTNLSKEHTVSTLDLYAEHFDPVLQFNETHKRRDLAKVAEMEKYRDLVTWADHLIFIFPIWWSGMPAILKGFIDRVFVADFAYSYKKVGLEGHLQGKSAWIITTHNTPSFAMPFVQDYGKVLKKQILKPCAISPVKLTELTSIEKISDDERQKLLHKVAQITRNILEHHHHHH 196
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190      


Chain D from PDB  Type:PROTEIN  Length:188
 aligned with Q8DTD1_STRMU | Q8DTD1 from UniProtKB/TrEMBL  Length:188

    Alignment length:188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
         Q8DTD1_STRMU     1 MKILIVYTHPNPTSFNAEILKQVQTNLSKEHTVSTLDLYAEHFDPVLQFNETHKRRDLAKVAEMEKYRDLVTWADHLIFIFPIWWSGMPAILKGFIDRVFVADFAYSYKKVGLEGHLQGKSAWIITTHNTPSFAMPFVQDYGKVLKKQILKPCAISPVKLTELTSIEKISDDERQKLLHKVAQITRNI 188
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Flavodoxin_2-3lcmD01 D:1-186                                                                                                                                                              -- Pfam domains (1)
           Pfam domains (2) Flavodoxin_2-3lcmD02 D:1-186                                                                                                                                                              -- Pfam domains (2)
           Pfam domains (3) Flavodoxin_2-3lcmD03 D:1-186                                                                                                                                                              -- Pfam domains (3)
           Pfam domains (4) Flavodoxin_2-3lcmD04 D:1-186                                                                                                                                                              -- Pfam domains (4)
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhh....eeeeee................hhhhhhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhh.....eeee..eeee.....eeeeeee......hhhhh...hhhhhhhh........eeeeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lcm D   1 MKILIVYTHPNPTSFNAEILKQVQTNLSKEHTVSTLDLYAEHFDPVLQFNETHKRRDLAKVAEMEKYRDLVTWADHLIFIFPIWWSGMPAILKGFIDRVFVADFAYSYKKVGLEGHLQGKSAWIITTHNTPSFAMPFVQDYGKVLKKQILKPCAISPVKLTELTSIEKISDDERQKLLHKVAQITRNI 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   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 3LCM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Flavoprotein (71)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8DTD1_STRMU | Q8DTD1)
molecular function
    GO:0003955    NAD(P)H dehydrogenase (quinone) activity    Catalysis of the reaction: NAD(P)H + H+ + a quinone = NAD(P)+ + a hydroquinone.
    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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 Related Entries

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        Q8DTD1_STRMU | Q8DTD1: 4f8y

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