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(-) Description

Title :  HIGH-RESOLUTION STRUCTURE OF PYRUVATE OXIDASE IN COMPLEX WITH REACTION INTERMEDIATE 2-HYDROXYETHYL-THIAMIN DIPHOSPHATE CARBANION-ENAMINE, CRYSTAL A
 
Authors :  D. Meyer, P. Neumann, E. Koers, H. Sjuts, S. Luedtke, G. M. Sheldrick, R. K. Tittmann
Date :  30 May 12  (Deposition) - 20 Jun 12  (Release) - 25 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.09
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, E. Koers, H. Sjuts, S. Ludtke, G. M. Sheldrick, R. Ficner, K. Tittmann
Unexpected Tautomeric Equilibria Of The Carbanion-Enamine Intermediate In Pyruvate Oxidase Highlight Unrecognized Chemical Versatility Of Thiamin.
Proc. Natl. Acad. Sci. Usa V. 109 10867 2012
PubMed-ID: 22730460  |  Reference-DOI: 10.1073/PNAS.1201280109

(-) Compounds

Molecule 1 - PYRUVATE OXIDASE
    Chains: A, B
    EC Number: 1.2.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: POX5, JDM1_2870
    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, 20)

Asymmetric Unit (6, 20)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL8Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
4PO42Ligand/IonPHOSPHATE ION
5PYR4Ligand/IonPYRUVIC ACID
6TDM2Ligand/Ion2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-HYDROXYETHYLIDENE)-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE
Biological Unit 1 (5, 36)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL16Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4PO44Ligand/IonPHOSPHATE ION
5PYR8Ligand/IonPYRUVIC ACID
6TDM4Ligand/Ion2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-HYDROXYETHYLIDENE)-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:555 , ARG A:556 , LEU A:557 , ASP A:558 , MET A:561 , SER A:562 , HOH A:977 , HOH A:1633 , HOH A:1687BINDING SITE FOR RESIDUE PYR A 701
02AC2SOFTWAREPHE A:121 , ASN A:263 , ARG A:264 , FAD A:709 , HOH A:1258 , HOH A:1488BINDING SITE FOR RESIDUE PYR A 702
03AC3SOFTWAREGLY A:34 , GLY A:35 , SER A:36 , SER A:82 , PHE A:111 , GLN A:122 , ILE A:480 , TDM A:708 , HOH A:909 , HOH A:956 , HOH A:1679 , HOH A:1766BINDING SITE FOR RESIDUE PO4 A 703
04AC4SOFTWARETRP A:24 , LYS A:75 , TYR A:158 , TYR A:189 , HOH A:1032 , HOH A:1684 , HOH B:7778BINDING SITE FOR RESIDUE GOL A 704
05AC5SOFTWARELYS A:433 , PRO A:437 , GLU A:438 , PRO A:466 , ALA A:533 , GLN A:534 , HOH A:1047 , HOH A:1225 , HOH A:1483BINDING SITE FOR RESIDUE GOL A 705
06AC6SOFTWAREARG A:156 , HIS A:160 , HOH A:849 , HOH A:894 , HOH A:1701 , ASN B:286 , LYS B:311 , LYS B:314 , HOH B:7143BINDING SITE FOR RESIDUE GOL A 706
07AC7SOFTWAREASP A:447 , ASN A:474 , GLN A:476 , TDM A:708 , HOH A:1632BINDING SITE FOR RESIDUE MG A 707
08AC8SOFTWAREPRO 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 , PO4 A:703 , MG A:707 , FAD A:709 , HOH A:813 , HOH A:822 , HOH A:847 , HOH A:1632BINDING SITE FOR RESIDUE TDM A 708
09AC9SOFTWAREHIS 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 , PRO A:288 , PHE A:289 , ASP A:306 , ILE A:307 , ASP A:308 , LYS A:311 , ALA A:324 , ASP A:325 , ALA A:326 , ASN A:398 , SER A:416 , ASN A:417 , PYR A:702 , TDM A:708 , HOH A:802 , HOH A:805 , HOH A:806 , HOH A:835 , HOH A:1350 , HOH A:1423 , HOH A:1642BINDING SITE FOR RESIDUE FAD A 709
10BC1SOFTWARETRP A:174 , THR A:487 , GLN A:489 , HOH A:978 , HOH A:1268 , HOH A:1630BINDING SITE FOR RESIDUE GOL A 710
11BC2SOFTWARELEU B:555 , ARG B:556 , LEU B:557 , ASP B:558 , MET B:561 , SER B:562 , HOH B:7219 , HOH B:7320 , HOH B:7670BINDING SITE FOR RESIDUE PYR B 701
12BC3SOFTWAREPHE B:121 , ASN B:263 , ARG B:264 , FAD B:710 , HOH B:7316 , HOH B:7680BINDING SITE FOR RESIDUE PYR B 702
13BC4SOFTWAREGLY B:34 , GLY B:35 , SER B:36 , SER B:82 , PHE B:111 , GLN B:122 , ILE B:480 , TDM B:709 , HOH B:7057 , HOH B:7131 , HOH B:7828BINDING SITE FOR RESIDUE PO4 B 703
14BC5SOFTWAREGLY B:25 , ASP B:27 , HIS B:28 , ASP B:69 , THR B:73 , LYS B:75 , ILE B:76 , ASN B:435 , HOH B:7034 , HOH B:7615 , HOH B:7802 , HOH B:7835BINDING SITE FOR RESIDUE GOL B 704
15BC6SOFTWAREHOH A:1012 , ALA B:569 , PHE B:570 , ARG B:573 , TYR B:574 , HOH B:7137 , HOH B:7144 , HOH B:7887BINDING SITE FOR RESIDUE GOL B 705
16BC7SOFTWARELYS B:433 , PRO B:437 , GLU B:438 , PRO B:466 , ALA B:533 , GLN B:534 , HOH B:7346 , HOH B:7638BINDING SITE FOR RESIDUE GOL B 706
17BC8SOFTWAREPRO B:409 , ARG B:412 , HOH B:7114 , HOH B:7178 , HOH B:7395 , HOH B:7575 , HOH B:7792BINDING SITE FOR RESIDUE GOL B 707
18BC9SOFTWAREASP B:447 , ASN B:474 , GLN B:476 , TDM B:709 , HOH B:7798BINDING SITE FOR RESIDUE MG B 708
19CC1SOFTWAREPRO 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 , PO4 B:703 , MG B:708 , FAD B:710 , HOH B:7010 , HOH B:7023 , HOH B:7045 , HOH B:7798BINDING SITE FOR RESIDUE TDM B 709
20CC2SOFTWAREHIS 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 , ALA B:324 , ASP B:325 , ALA B:326 , ASN B:398 , SER B:416 , ASN B:417 , PYR B:702 , TDM B:709 , HOH B:7001 , HOH B:7003 , HOH B:7015 , HOH B:7019 , HOH B:7611 , HOH B:7675 , HOH B:7739BINDING SITE FOR RESIDUE FAD B 710

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FEG)

(-) 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:583
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4fega1 A:9-182 automated matches                                                                                                                                             d4fega2 A:183-365 automated matches                                                                                                                                                    d4fega3 A:366-591 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
                 4feg A   9 TNILAGAAVIKVLEAWGVDHLYGIPGGSINSIMDALSAERDRIHYIQVRHEEVGAMAAAADAKLTGKIGVCFGSAGPGGTHLMNGLYDAREDHVPVLALIGQFGTTGMNMDTFQEMNENPIYADVADYNVTAVNAATLPHVIDEAIRRAYAHQGVAVVQIPVDLPWQQIPAEDWYASANSYQTPLLPEPDVQAVTRLTQTLLAAERPLIYYGIGARKAGKELEQLSKTLKIPLMSTYPAKGIVADRYPAYLGSANRVAQKPANEALAQADVVLFVGNNYPFAEVSKAFKNTRYFLQIDIDPAKLGKRHKTDIAVLADAQKTLAAILAQVSERESTPWWQANLANVKNWRAYLASLEDKQEGPLQAYQVLRAVNKIAEPDAIYSIDVGDINLNANRHLKLTPSNRHITSNLFATMGVGIPGAIAAKLNYPERQVFNLAGDGGASMTMQDLATQVQYHLPVINVVFTNCQYGFIKDEQEDTNQNDFIGVEFNDIDFSKIADGVHMQAFRVNKIEQLPDVFEQAKAIAQHEPVLIDAVITGDRPLPAEKLRLDSAMSSAADIEAFKQRYEAQDLQPLSTYLKQFGL 591
                                    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:583
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4fegb1 B:9-182 automated matches                                                                                                                                             d4fegb2 B:183-365 automated matches                                                                                                                                                    d4fegb3 B:366-591 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....eeeeeehhhhhhhh.hhhhhhhh....eeeeee...hhhhhhhhhhhh............hhhhhhhhh..eeeee.hhhhhhhhhhhhhhhh....eeeeee...................hhhhhhhhhhhh......hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4feg B   9 TNILAGAAVIKVLEAWGVDHLYGIPGGSINSIMDALSAERDRIHYIQVRHEEVGAMAAAADAKLTGKIGVCFGSAGPGGTHLMNGLYDAREDHVPVLALIGQFGTTGMNMDTFQEMNENPIYADVADYNVTAVNAATLPHVIDEAIRRAYAHQGVAVVQIPVDLPWQQIPAEDWYASANSYQTPLLPEPDVQAVTRLTQTLLAAERPLIYYGIGARKAGKELEQLSKTLKIPLMSTYPAKGIVADRYPAYLGSANRVAQKPANEALAQADVVLFVGNNYPFAEVSKAFKNTRYFLQIDIDPAKLGKRHKTDIAVLADAQKTLAAILAQVSERESTPWWQANLANVKNWRAYLASLEDKQEGPLQAYQVLRAVNKIAEPDAIYSIDVGDINLNANRHLKLTPSNRHITSNLFATMGVGIPGAIAAKLNYPERQVFNLAGDGGASMTMQDLATQVQYHLPVINVVFTNCQYGFIKDEQEDTNQNDFIGVEFNDIDFSKIADGVHMQAFRVNKIEQLPDVFEQAKAIAQHEPVLIDAVITGDRPLPAEKLRLDSAMSSAADIEAFKQRYEAQDLQPLSTYLKQFGL 591
                                    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 4FEG)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

1pow PYRUVATE OXIDASE WILD-TYPE
1pox PYRUVATE OXIDASE, STABILIZED MUTANT
2ez4 PYRUVATE OXIDASE VARIANT F479W
2ez8 PYRUVATE OXIDASE VARIANT F479W IN COMPLEX WITH REACTION INTERMEDIATE 2-LACTYL-THIAMIN DIPHOSPHATE
2ez9 PYRUVATE OXIDASE VARIANT F479W IN COMPLEX WITH REACTION INTERMEDIATE ANALOGUE 2-PHOSPHONOLACTYL-THIAMIN DIPHOSPHATE
2ezt PYRUVATE OXIDASE VARIANT F479W IN COMPLEX WITH REACTION INTERMEDIATE 2-HYDROXYETHYL-THIAMIN DIPHOSPHATE
2ezu PYRUVATE OXIDASE VARIANT F479W IN COMPLEX WITH REACTION INTERMEDIATE 2-ACETYL-THIAMIN DIPHOSPHATE
4fee