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(-) Description

Title :  HIGH-RESOLUTION CRYSTAL STRUCTURE OF PYRUVATE OXIDASE FROM L. PLANTARUM IN COMPLEX WITH PHOSPHATE
 
Authors :  P. Neumann, K. Tittmann
Date :  29 Apr 13  (Deposition) - 12 Jun 13  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.06
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Carbanion, Structure Activity Relationship, Oxidation-Reduction, Umpolung, Thiamine Diphosphate, Reaction Intermediate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Meyer, P. Neumann, R. Ficner, K. Tittmann
Observation Of A Stable Carbene At The Active Site Of A Thiamin Enzyme.
Nat. Chem. Biol. V. 9 488 2013
PubMed-ID: 23748673  |  Reference-DOI: 10.1038/NCHEMBIO.1275

(-) Compounds

Molecule 1 - PYRUVATE OXIDASE
    Chains: A, B
    EC Number: 1.2.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: JDM1_2870, POX5
    Organism Scientific: LACTOBACILLUS PLANTARUM
    Organism Taxid: 644042
    Strain: JDM1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 18)

Asymmetric Unit (6, 18)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL9Ligand/IonGLYCEROL
3K1Ligand/IonPOTASSIUM ION
4MG2Ligand/IonMAGNESIUM ION
5PO42Ligand/IonPHOSPHATE ION
6TDP2Ligand/IonTHIAMIN DIPHOSPHATE
Biological Unit 1 (4, 30)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL18Ligand/IonGLYCEROL
3K-1Ligand/IonPOTASSIUM ION
4MG-1Ligand/IonMAGNESIUM ION
5PO44Ligand/IonPHOSPHATE ION
6TDP4Ligand/IonTHIAMIN DIPHOSPHATE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:101 , PHE A:121 , GLY A:220 , ILE A:221 , GLY A:222 , THR A:244 , TYR A:245 , ALA A:262 , ASN A:263 , ARG A:264 , VAL A:265 , GLY A:284 , ASN A:285 , ASN A:286 , TYR A:287 , PRO A:288 , PHE A:289 , ASP A:306 , ILE A:307 , ASP A:308 , LYS A:311 , ASP A:325 , ALA A:326 , ASN A:398 , SER A:416 , ASN A:417 , HOH A:802 , HOH A:811 , HOH A:847 , HOH A:1078 , HOH A:1079 , HOH A:1184 , HOH A:1202 , HOH A:1342 , HOH A:1485BINDING SITE FOR RESIDUE FAD A 701
02AC2SOFTWAREASP A:447 , ASN A:474 , GLN A:476 , TDP A:704 , HOH A:803BINDING SITE FOR RESIDUE MG A 702
03AC3SOFTWAREGLY A:34 , GLY A:35 , SER A:36 , SER A:82 , PHE A:111 , GLN A:122 , ILE A:480 , TDP A:704 , HOH A:912 , HOH A:1019 , HOH A:1487 , HOH A:1598BINDING SITE FOR RESIDUE PO4 A 703
04AC4SOFTWAREPRO A:33 , GLU A:59 , SER A:82 , PRO A:85 , HIS A:89 , GLN A:122 , VAL A:394 , ASP A:396 , ALA A:420 , MET A:422 , GLY A:446 , ASP A:447 , GLY A:448 , GLY A:449 , ASN A:474 , GLN A:476 , TYR A:477 , GLY A:478 , PHE A:479 , ILE A:480 , MG A:702 , PO4 A:703 , HOH A:803 , HOH A:820 , HOH A:824 , HOH A:846 , HOH A:1487BINDING SITE FOR RESIDUE TDP A 704
05AC5SOFTWAREALA A:23 , TRP A:24 , LYS A:75 , TYR A:158 , ALA A:186 , TYR A:189 , HOH A:1024 , HOH A:1421BINDING SITE FOR RESIDUE GOL A 705
06AC6SOFTWARELYS A:433 , PRO A:437 , GLU A:438 , PRO A:466 , ALA A:533 , GLN A:534 , HOH A:1089 , HOH A:1121 , HOH A:1373BINDING SITE FOR RESIDUE GOL A 706
07AC7SOFTWARETRP A:174 , THR A:487 , GLN A:489 , HOH A:1291 , HOH A:1444BINDING SITE FOR RESIDUE GOL A 707
08AC8SOFTWAREARG A:264 , GLU A:483 , ASP A:486 , GLU A:553 , HOH A:1029 , HOH A:1222 , HOH A:1347 , HOH A:1483 , HOH A:1496 , HOH A:1629BINDING SITE FOR RESIDUE GOL A 708
09AC9SOFTWAREMET A:452 , GLN A:455 , HOH A:825BINDING SITE FOR RESIDUE K A 709
10BC1SOFTWAREHIS B:101 , PHE B:121 , GLY B:220 , ILE B:221 , GLY B:222 , THR B:244 , TYR B:245 , PRO B:246 , ALA B:262 , ASN B:263 , ARG B:264 , VAL B:265 , GLY B:284 , ASN B:285 , ASN B:286 , TYR B:287 , PRO B:288 , PHE B:289 , ASP B:306 , ILE B:307 , ASP B:308 , LYS B:311 , ASP B:325 , ALA B:326 , ASN B:398 , SER B:416 , ASN B:417 , HOH B:801 , HOH B:807 , HOH B:816 , HOH B:819 , HOH B:1132 , HOH B:1133 , HOH B:1336 , HOH B:1498 , HOH B:1553BINDING SITE FOR RESIDUE FAD B 701
11BC2SOFTWAREASP B:447 , ASN B:474 , GLN B:476 , TDP B:703 , HOH B:802BINDING SITE FOR RESIDUE MG B 702
12BC3SOFTWAREPRO B:33 , GLU B:59 , SER B:82 , PRO B:85 , HIS B:89 , GLN B:122 , VAL B:394 , ASP B:396 , ALA B:420 , MET B:422 , GLY B:446 , ASP B:447 , GLY B:448 , GLY B:449 , ASN B:474 , GLN B:476 , TYR B:477 , GLY B:478 , PHE B:479 , ILE B:480 , MG B:702 , PO4 B:704 , HOH B:802 , HOH B:817 , HOH B:821 , HOH B:855 , HOH B:1496BINDING SITE FOR RESIDUE TDP B 703
13BC4SOFTWAREGLY B:34 , GLY B:35 , SER B:36 , SER B:82 , PHE B:111 , GLN B:122 , ILE B:480 , TDP B:703 , HOH B:873 , HOH B:1030 , HOH B:1356 , HOH B:1496BINDING SITE FOR RESIDUE PO4 B 704
14BC5SOFTWARELYS B:433 , PRO B:437 , GLU B:438 , PRO B:466 , ALA B:533 , GLN B:534 , HOH B:1176 , HOH B:1235BINDING SITE FOR RESIDUE GOL B 705
15BC6SOFTWARETHR B:487 , HOH B:1306 , HOH B:1712BINDING SITE FOR RESIDUE GOL B 706
16BC7SOFTWAREHOH A:1083 , ALA B:569 , PHE B:570 , ARG B:573 , TYR B:574 , HOH B:961 , HOH B:980 , HOH B:1187 , HOH B:1379BINDING SITE FOR RESIDUE GOL B 707
17BC8SOFTWAREPRO B:409 , SER B:410 , ASN B:411 , ARG B:412 , TYR B:436 , ARG B:439 , GOL B:709BINDING SITE FOR RESIDUE GOL B 708
18BC9SOFTWAREPRO B:409 , ARG B:412 , GOL B:708 , HOH B:917 , HOH B:939 , HOH B:996 , HOH B:1558BINDING SITE FOR RESIDUE GOL B 709

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KGD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4KGD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KGD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KGD)

(-) Exons   (0, 0)

(no "Exon" information available for 4KGD)

(-) 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:586
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4kgda1 A:9-182 automated matches                                                                                                                                             d4kgda2 A:183-365 automated matches                                                                                                                                                    d4kgda3 A:366-594 automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhh...eeee..hhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhh...eeeeeee...............hhhhhh....eeee.....hhhhhhhhhhhhhhhhh.eeeeeee.hhhh.eee......hhhhh........hhhhhhhhhhhhhhh..eeeee.hhhh.hhhhhhhhhhhhh..eee.hhhh..................hhhhhhhhhhh.eeeee.................eeeeee.hhhhh.......eeee.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh....eeee..hhhhhhhhhhh......eee.........hhhhhhhhhhhhh....eeeeeehhhhhhhh.hhhhhhhh....eeeeee...hhhhhhhhhhhh............hhhhhhhhh..eeeee.hhhhhhhhhhhhhhhh....eeeeee...................hhhhhhhhhhhhh.....hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kgd A   9 TNILAGAAVIKVLEAWGVDHLYGIPGGSINSIMDALSAERDRIHYIQVRHEEVGAMAAAADAKLTGKIGVCFGSAGPGGTHLMNGLYDAREDHVPVLALIGQFGTTGMNMDTFQEMNENPIYADVADYNVTAVNAATLPHVIDEAIRRAYAHQGVAVVQIPVDLPWQQIPAEDWYASANSYQTPLLPEPDVQAVTRLTQTLLAAERPLIYYGIGARKAGKELEQLSKTLKIPLMSTYPAKGIVADRYPAYLGSANRVAQKPANEALAQADVVLFVGNNYPFAEVSKAFKNTRYFLQIDIDPAKLGKRHKTDIAVLADAQKTLAAILAQVSERESTPWWQANLANVKNWRAYLASLEDKQEGPLQAYQVLRAVNKIAEPDAIYSIDVGDINLNANRHLKLTPSNRHITSNLFATMGVGIPGAIAAKLNYPERQVFNLAGDGGASMTMQDLATQVQYHLPVINVVFTNCQYGFIKDEQEDTNQNDFIGVEFNDIDFSKIADGVHMQAFRVNKIEQLPDVFEQAKAIAQHEPVLIDAVITGDRPLPAEKLRLDSAMSSAADIEAFKQRYEAQDLQPLSTYLKQFGLDDL 594
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588      


Chain B from PDB  Type:PROTEIN  Length:585
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4kgdb1 B:9-182 automated matches                                                                                                                                             d4kgdb2 B:183-365 automated matches                                                                                                                                                    d4kgdb3 B:366-593 automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhh...eeee..hhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhh...eeeeeee...............hhhhhh....eeee.....hhhhhhhhhhhhhhhhh.eeeeeee.hhhh.eee......hhhhh........hhhhhhhhhhhhhhh..eeeee.hhhh.hhhhhhhhhhhhh..eee.hhhh..................hhhhhhhhhhh.eeeee.................eeeeee.hhhhh.......eeee.hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh....eeee..hhhhhhhhhhh......eee.........hhhhhhhhhhhhh....eeeeeehhhhhhh..hhhhhhhh....eeeeee...hhhhhhhhhhhh............hhhhhhhhh..eeeee.hhhhhhhhhhhhhhhh....eeeeee...................hhhhhhhhhhhhh.....hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kgd B   9 TNILAGAAVIKVLEAWGVDHLYGIPGGSINSIMDALSAERDRIHYIQVRHEEVGAMAAAADAKLTGKIGVCFGSAGPGGTHLMNGLYDAREDHVPVLALIGQFGTTGMNMDTFQEMNENPIYADVADYNVTAVNAATLPHVIDEAIRRAYAHQGVAVVQIPVDLPWQQIPAEDWYASANSYQTPLLPEPDVQAVTRLTQTLLAAERPLIYYGIGARKAGKELEQLSKTLKIPLMSTYPAKGIVADRYPAYLGSANRVAQKPANEALAQADVVLFVGNNYPFAEVSKAFKNTRYFLQIDIDPAKLGKRHKTDIAVLADAQKTLAAILAQVSERESTPWWQANLANVKNWRAYLASLEDKQEGPLQAYQVLRAVNKIAEPDAIYSIDVGDINLNANRHLKLTPSNRHITSNLFATMGVGIPGAIAAKLNYPERQVFNLAGDGGASMTMQDLATQVQYHLPVINVVFTNCQYGFIKDEQEDTNQNDFIGVEFNDIDFSKIADGVHMQAFRVNKIEQLPDVFEQAKAIAQHEPVLIDAVITGDRPLPAEKLRLDSAMSSAADIEAFKQRYEAQDLQPLSTYLKQFGLDD 593
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588
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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  (2, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KGD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KGD)

(-) Gene Ontology  (0, 0)

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(-) Related Entries Specified in the PDB File

4fee HIGH-RESOLUTION STRUCTURE OF PYRUVATE OXIDASE IN COMPLEX WITH REACTION INTERMEDIATE 2-HYDROXYETHYL-THIAMIN DIPHOSPHATE CARBANION-ENAMINE