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(-) Description

Title :  THE REFINED STRUCTURES OF A STABILIZED MUTANT AND OF WILD-TYPE PYRUVATE OXIDASE FROM LACTOBACILLUS PLANTARUM
 
Authors :  Y. A. Muller, G. E. Schulz
Date :  09 Nov 93  (Deposition) - 31 Jan 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Oxidoreductase(Oxygen As Acceptor) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. A. Muller, G. Schumacher, R. Rudolph, G. E. Schulz
The Refined Structures Of A Stabilized Mutant And Of Wild-Type Pyruvate Oxidase From Lactobacillus Plantarum.
J. Mol. Biol. V. 237 315 1994
PubMed-ID: 8145244  |  Reference-DOI: 10.1006/JMBI.1994.1233
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYRUVATE OXIDASE
    Chains: A, B
    EC Number: 1.2.3.3
    Engineered: YES
    Organism Scientific: LACTOBACILLUS PLANTARUM
    Organism Taxid: 1590

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MG2Ligand/IonMAGNESIUM ION
3TPP2Ligand/IonTHIAMINE DIPHOSPHATE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MG-1Ligand/IonMAGNESIUM ION
3TPP4Ligand/IonTHIAMINE DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:447 , ASN A:474 , GLN A:476 , TPP A:611BINDING SITE FOR RESIDUE MG A 610
2AC2SOFTWAREASP B:447 , ASN B:474 , GLN B:476 , TPP B:611BINDING SITE FOR RESIDUE MG B 610
3AC3SOFTWAREPRO A:33 , GLU A:59 , SER A:82 , PRO A:85 , HIS A:89 , GLN A:122 , ASP A:396 , ALA A:420 , MET A:422 , 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:610 , HOH A:617 , HOH A:659 , HOH A:664BINDING SITE FOR RESIDUE TPP A 611
4AC4SOFTWAREHIS 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 , LYS A:311 , ASP A:325 , ALA A:326 , ASN A:398 , SER A:416 , ASN A:417 , HOH A:614 , HOH A:635BINDING SITE FOR RESIDUE FAD A 612
5AC5SOFTWAREPRO B:33 , GLU B:59 , SER B:82 , PRO B:85 , HIS B:89 , GLN B:122 , ASP B:396 , ALA B:420 , MET B:422 , GLY B:446 , ASP B:447 , GLY B:448 , GLY B:449 , MET B:452 , ASN B:474 , GLN B:476 , TYR B:477 , GLY B:478 , PHE B:479 , ILE B:480 , MG B:610 , HOH B:635 , HOH B:651 , HOH B:662BINDING SITE FOR RESIDUE TPP B 611
6AC6SOFTWAREHIS 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 , LYS B:311 , ASP B:325 , ALA B:326 , ASN B:398 , SER B:416 , ASN B:417 , HOH B:640BINDING SITE FOR RESIDUE FAD B 612

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1POW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1POW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1POW)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPP_ENZYMESPS00187 Thiamine pyrophosphate enzymes signature.POXB_LACPL430-449
 		  2A:430-449
B:430-449
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPP_ENZYMESPS00187 Thiamine pyrophosphate enzymes signature.POXB_LACPL430-449
 		  4A:430-449
B:430-449

(-) Exons   (0, 0)

(no "Exon" information available for 1POW)

(-) 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:585
 aligned with POXB_LACPL | P37063 from UniProtKB/Swiss-Prot  Length:603

    Alignment length:585
                                    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     
           POXB_LACPL     9 TNILAGAAVIKVLEAWGVDHLYGIPGGSINSIMDALSAERDRIHYIQVRHEEVGAMAAAADAKLTGKIGVCFGSAGPGGTHLMNGLYDAREDHVPVLALIGQFGTTGMNMDTFQEMNENPIYADVADYNVTAVNAATLPHVIDEAIRRAYAHQGVAVVQIPVDLPWQQIPAEDWYASANSYQTPLLPEPDVQAVTRLTQTLLAAERPLIYYGIGARKAGKELEQLSKTLKIPLMSTYPAKGIVADRYPAYLGSANRVAQKPANEALAQADVVLFVGNNYPFAEVSKAFKNTRYFLQIDIDPAKLGKRHKTDIAVLADAQKTLAAILAQVSERESTPWWQANLANVKNWRAYLASLEDKQEGPLQAYQVLRAVNKIAEPDAIYSIDVGDINLNANRHLKLTPSNRHITSNLFATMGVGIPGAIAAKLNYPERQVFNLAGDGGASMTMQDLATQVQYHLPVINVVFTNCQYGFIKDEQEDTNQNDFIGVEFNDIDFSKIADGVHMQAFRVNKIEQLPDVFEQAKAIAQHEPVLIDAVITGDRPLPAEKLRLDSATSSAADIEAFKQRYEAQDLQPLSTYLKQFGLDD 593
               SCOP domains d1powa2 A:9-182 Pyruvate oxidase                                                                                                                                              d1powa1 A:183-365 Pyruvate oxidase                                                                                                                                                     d1powa3 A:366-593 Pyruvate oxidase                                                                                                                                                                                                   SCOP domains
               CATH domains 1powA01 A:9-192  [code=3.40.50.970, no name defined]                                                                                                                                    1powA02 A:193-359 TPP-binding domain                                                                                                                                   1powA03 A:360-549  [code=3.40.50.970, no name defined]                                                                                                                                        -------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeehhhhhhhhhhhh.eeeee.....hhhhhhhhh......eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhh.eeeeeeee.........................eeeee....hhhhhhhhhhhhhhhhheeeeeeeee....eeeee..................hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh.eeeee............eeee.......hhhhhhhhh.eeeeeee................eeeeee.............eeeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeee..hhhhhhhhhh......eee..........hhhhhhhhhhhh...eeeeeehhhhhhhhh...hhhhhhh..eeeeeee...hhhhhhhhhhhh............hhhhhhhhhh.eeeee.....hhhhhhhhhhhh....eeeeeee..................hhhhhhhhhhhhh......hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pow A   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     


Chain B from PDB  Type:PROTEIN  Length:585
 aligned with POXB_LACPL | P37063 from UniProtKB/Swiss-Prot  Length:603

    Alignment length:585
                                    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     
           POXB_LACPL     9 TNILAGAAVIKVLEAWGVDHLYGIPGGSINSIMDALSAERDRIHYIQVRHEEVGAMAAAADAKLTGKIGVCFGSAGPGGTHLMNGLYDAREDHVPVLALIGQFGTTGMNMDTFQEMNENPIYADVADYNVTAVNAATLPHVIDEAIRRAYAHQGVAVVQIPVDLPWQQIPAEDWYASANSYQTPLLPEPDVQAVTRLTQTLLAAERPLIYYGIGARKAGKELEQLSKTLKIPLMSTYPAKGIVADRYPAYLGSANRVAQKPANEALAQADVVLFVGNNYPFAEVSKAFKNTRYFLQIDIDPAKLGKRHKTDIAVLADAQKTLAAILAQVSERESTPWWQANLANVKNWRAYLASLEDKQEGPLQAYQVLRAVNKIAEPDAIYSIDVGDINLNANRHLKLTPSNRHITSNLFATMGVGIPGAIAAKLNYPERQVFNLAGDGGASMTMQDLATQVQYHLPVINVVFTNCQYGFIKDEQEDTNQNDFIGVEFNDIDFSKIADGVHMQAFRVNKIEQLPDVFEQAKAIAQHEPVLIDAVITGDRPLPAEKLRLDSATSSAADIEAFKQRYEAQDLQPLSTYLKQFGLDD 593
               SCOP domains d1powb2 B:9-182 Pyruvate oxidase                                                                                                                                              d1powb1 B:183-365 Pyruvate oxidase                                                                                                                                                     d1powb3 B:366-593 Pyruvate oxidase                                                                                                                                                                                                   SCOP domains
               CATH domains 1powB01 B:9-192  [code=3.40.50.970, no name defined]                                                                                                                                    1powB02 B:193-359 TPP-binding domain                                                                                                                                   1powB03 B:360-549  [code=3.40.50.970, no name defined]                                                                                                                                        -------------------------------------------- CATH domains
           Pfam domains (1) --TPP_enzyme_N-1powB05 B:11-181                                                                                                                                              --------------------TPP_enzyme_M-1powB01 B:202-333                                                                                                      -----------------------------------------------------------TPP_enzyme_C-1powB03 B:393-542                                                                                                                        --------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --TPP_enzyme_N-1powB06 B:11-181                                                                                                                                              --------------------TPP_enzyme_M-1powB02 B:202-333                                                                                                      -----------------------------------------------------------TPP_enzyme_C-1powB04 B:393-542                                                                                                                        --------------------------------------------------- Pfam domains (2)
         Sec.struct. author eeeeehhhhhhhhhhhh.eeeee.....hhhhhhhhh......eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhh.eeeeeeee.........................eeeee....hhhhhhhhhhhhhhhhheeeeeeeee....eeeee..................hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh.eeeee............eeee.......hhhhhhhhh.eeeeeee................eeeeee.............eeeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeee..hhhhhhhhhh......eee..........hhhhhhhhhhhh...eeeeeehhhhhhhhh...hhhhhhh..eeeeeee...hhhhhhhhhhhh............hhhhhhhhhh.eeeee.....hhhhhhhhhhhh....eeeeeee..................hhhhhhhhhhhhh......hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pow 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  (3, 6)

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

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (3, 6)

Asymmetric Unit
(-)
Clan: FAD_DHS (82)
(-)
Clan: THDP-binding (106)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (POXB_LACPL | P37063)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    GO:0047112    pyruvate oxidase activity    Catalysis of the reaction: H(+) + O(2) + phosphate + pyruvate = acetyl phosphate + CO(2) + H(2)O(2).
    GO:0030976    thiamine pyrophosphate binding    Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
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

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

UniProtKB/Swiss-Prot
        POXB_LACPL | P37063: 1pox 1y9d 2ez4 2ez8 2ez9 2ezt 2ezu

(-) Related Entries Specified in the PDB File

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