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(-) Description

Title :  CRYSTAL STRUCTURE OF ZYMOMONAS MOBILIS PYRUVATE DECARBOXYLASE VARIANT GLU473ALA
 
Authors :  C. Wechsler, P. Neumann, K. Tittmann
Date :  07 May 15  (Deposition) - 04 Nov 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Thiamin Diphosphate (Thdp), Pyruvate Decarboxylase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Wechsler, D. Meyer, S. Loschonsky, L. M. Funk, P. Neumann, R. Ficner F. Brodhun, M. Muller, K. Tittmann
Tuning And Switching Enantioselectivity Of Asymmetric Carboligation In An Enzyme Through Mutational Analysis Of A Single Hot Spot.
Chembiochem V. 16 2580 2015
PubMed-ID: 26488818  |  Reference-DOI: 10.1002/CBIC.201500529

(-) Compounds

Molecule 1 - PYRUVATE DECARBOXYLASE
    Chains: A, B, C, D
    EC Number: 4.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PDC, ZMO1360
    Mutation: YES
    Organism Scientific: ZYMOMONAS MOBILIS
    Organism Taxid: 542
    Synonym: PDC

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MG4Ligand/IonMAGNESIUM ION
3NI2Ligand/IonNICKEL (II) ION
4TPP4Ligand/IonTHIAMINE DIPHOSPHATE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:440 , ASN A:467 , GLY A:469 , TPP A:603 , HOH A:795binding site for residue MG A 601
02AC2SOFTWAREHIS A:106 , HIS A:122 , HIS C:106 , HIS C:122binding site for residue NI A 602
03AC3SOFTWAREASP A:390 , GLY A:413 , HIS A:414 , ILE A:415 , GLY A:439 , ASP A:440 , GLY A:441 , SER A:442 , ASN A:467 , GLY A:469 , TYR A:470 , THR A:471 , ILE A:472 , MG A:601 , HOH A:727 , HOH A:795 , HOH A:801 , ALA B:25 , GLY B:26 , GLU B:50 , VAL B:75 , HIS B:114binding site for residue TPP A 603
04AC4SOFTWAREASP B:440 , ASN B:467 , GLY B:469 , TPP B:604 , HOH B:713binding site for residue MG B 601
05AC5SOFTWAREHIS B:106 , HIS B:122 , HOH B:811 , HIS D:106 , HIS D:122binding site for residue NI B 602
06AC6SOFTWAREALA B:89 , GLU B:90 , ASN B:91 , SER B:218 , ALA B:245 , TYR B:408 , MET B:410 , GLN B:411 , HOH B:714binding site for residue GOL B 603
07AC7SOFTWAREALA A:25 , GLY A:26 , GLU A:50 , VAL A:75 , HIS A:114 , GLY B:389 , ASP B:390 , GLY B:413 , HIS B:414 , ILE B:415 , GLY B:439 , ASP B:440 , GLY B:441 , SER B:442 , ASN B:467 , GLY B:469 , TYR B:470 , THR B:471 , ILE B:472 , MG B:601 , HOH B:713binding site for residue TPP B 604
08AC8SOFTWAREASP C:440 , ASN C:467 , GLY C:469 , TPP C:603 , HOH C:751binding site for residue MG C 601
09AC9SOFTWARETYR C:425 , ALA C:429 , GLU C:431binding site for residue GOL C 602
10AD1SOFTWAREGLY C:389 , ASP C:390 , GLY C:413 , HIS C:414 , ILE C:415 , GLY C:439 , ASP C:440 , GLY C:441 , SER C:442 , ASN C:467 , GLY C:469 , TYR C:470 , THR C:471 , ILE C:472 , MG C:601 , HOH C:751 , HOH C:776 , HOH C:827 , ALA D:25 , GLY D:26 , GLU D:50 , VAL D:75 , HIS D:114binding site for residue TPP C 603
11AD2SOFTWAREASP D:440 , ASN D:467 , GLY D:469 , TPP D:602binding site for residue MG D 601
12AD3SOFTWAREALA C:25 , GLU C:50 , VAL C:75 , HIS C:114 , GLY D:389 , ASP D:390 , GLY D:413 , HIS D:414 , ILE D:415 , GLY D:439 , ASP D:440 , GLY D:441 , SER D:442 , ASN D:467 , GLY D:469 , TYR D:470 , THR D:471 , ILE D:472 , MG D:601 , HOH D:794binding site for residue TPP D 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZP1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4ZP1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZP1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZP1)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZP1)

(-) Sequences/Alignments

Asymmetric/Biological 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:565
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhhh...eeee.....hhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh...eeeeeee.hhhhh...............hhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhhh..eeeeee.hhh..ee.ee..hhhhhh....hhhhhhhhhhhhhhhh.....eeeee........hhhhhhhhhhhhh.eeeee.hhh.........eeeeehhhhh..hhhhhhhhh.eeeee....................eeee...eeee..eeee..hhhhhhhhhhhhh...hhhhhhhhhhh................hhhhhhhhhhh.....eeeee..hhhhhhhhh.......eee.........hhhhhhhhhhhhh...eeeeeeehhhhhhhh.hhhhhhhh....eeeeee...hhhhhh...hhhhh....hhhhhhhhhhh.........eeeee.hhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zp1 A   2 SYTVGTYLAERLVQIGLKHHFAVAGDYNLVLLDNLLLNKNMEQVYCCNELNCGFSAEGYARAKGAAAAVVTYSVGALSAFDAIGGAYAENLPVILISGAPNNNDHAAGHVLHHALGKTDYHYQLEMAKNITAAAEAIYTPEEAPAKIDHVIKTALREKKPVYLEIACNIASMPCAAPGPASALFNDEASDEASLNAAVEETLKFIANRDKVAVLVGSKLRAAGAEEAAVKFADALGGAVATMAAAKSFFPEENPHYIGTSWGEVSYPGVEKTMKEADAVIALAPVFNDYSTTGWTDIPDPKKLVLAEPRSVVVNGIRFPSVHLKDYLTRLAQKVSKKTGALDFFKSLNAGELKKAAPADPSAPLVNAEIARQVEALLTPNTTVIAETGDSWFNAQRMKLPNGARVEYEMQWGHIGWSVPAAFGYAVGAPERRNILMVGDGSFQLTAQEVAQMVRLKLPVIIFLINNYGYTIAVMIHDGPYNNIKNWDYAGLMEVFNGNGGYDSGAGKGLKAKTGGELAEAIKVALANTDGPTLIECFIGREDCTEELVKWGKRVAAANSRKPVNK 566
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561     


Chain B from PDB  Type:PROTEIN  Length:565
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhhh...eeee.....hhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh...eeeeeee.hhhhh...............hhhhhhhh.....eeee.hhhhhhhhhhhhhhhhhhhh..eeeeee......ee.ee.hhhhhh.....hhhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhh.eeee.hhhh.........eeee.hhhhh..hhhhhhhhh.eeeee....................eeee...eeee..eeee..hhhhhhhhhhhhh...hhhhhhhhhh.................hhhhhhhhhhh.....eeeee...hhhhhhhh.......eee.........hhhhhhhhhhhhh...eeeeeeehhhhhhhh.hhhhhhhh....eeeeee...hhhhhh...hhhhh....hhhhhhhhhhh.........eeeee.hhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zp1 B   2 SYTVGTYLAERLVQIGLKHHFAVAGDYNLVLLDNLLLNKNMEQVYCCNELNCGFSAEGYARAKGAAAAVVTYSVGALSAFDAIGGAYAENLPVILISGAPNNNDHAAGHVLHHALGKTDYHYQLEMAKNITAAAEAIYTPEEAPAKIDHVIKTALREKKPVYLEIACNIASMPCAAPGPASALFNDEASDEASLNAAVEETLKFIANRDKVAVLVGSKLRAAGAEEAAVKFADALGGAVATMAAAKSFFPEENPHYIGTSWGEVSYPGVEKTMKEADAVIALAPVFNDYSTTGWTDIPDPKKLVLAEPRSVVVNGIRFPSVHLKDYLTRLAQKVSKKTGALDFFKSLNAGELKKAAPADPSAPLVNAEIARQVEALLTPNTTVIAETGDSWFNAQRMKLPNGARVEYEMQWGHIGWSVPAAFGYAVGAPERRNILMVGDGSFQLTAQEVAQMVRLKLPVIIFLINNYGYTIAVMIHDGPYNNIKNWDYAGLMEVFNGNGGYDSGAGKGLKAKTGGELAEAIKVALANTDGPTLIECFIGREDCTEELVKWGKRVAAANSRKPVNK 566
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561     


Chain C from PDB  Type:PROTEIN  Length:565
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhhh...eeee.....hhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh...eeeeeee.....................hhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhh..eeeeee.hhh..ee.ee..hhhhhh....hhhhhhhhhhhhhhhh.....eeeee........hhhhhhhhhhhhh.eeeee.hhh.........eeeeehhhhh..hhhhhhhh..eeeee....................eeeee..eeee..eeee..hhhhhhhhhhhhh...hhhhhhhhhhh................hhhhhhhhhhh.....eeeee..hhhhhhhhh.......eee.........hhhhhhhhhhhhh...eeeeeeehhhhhhhh.hhhhhhhh....eeeeee...hhhhhh...hhhhh.......hhhhhhhh.........eeeee.hhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zp1 C   2 SYTVGTYLAERLVQIGLKHHFAVAGDYNLVLLDNLLLNKNMEQVYCCNELNCGFSAEGYARAKGAAAAVVTYSVGALSAFDAIGGAYAENLPVILISGAPNNNDHAAGHVLHHALGKTDYHYQLEMAKNITAAAEAIYTPEEAPAKIDHVIKTALREKKPVYLEIACNIASMPCAAPGPASALFNDEASDEASLNAAVEETLKFIANRDKVAVLVGSKLRAAGAEEAAVKFADALGGAVATMAAAKSFFPEENPHYIGTSWGEVSYPGVEKTMKEADAVIALAPVFNDYSTTGWTDIPDPKKLVLAEPRSVVVNGIRFPSVHLKDYLTRLAQKVSKKTGALDFFKSLNAGELKKAAPADPSAPLVNAEIARQVEALLTPNTTVIAETGDSWFNAQRMKLPNGARVEYEMQWGHIGWSVPAAFGYAVGAPERRNILMVGDGSFQLTAQEVAQMVRLKLPVIIFLINNYGYTIAVMIHDGPYNNIKNWDYAGLMEVFNGNGGYDSGAGKGLKAKTGGELAEAIKVALANTDGPTLIECFIGREDCTEELVKWGKRVAAANSRKPVNK 566
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561     


Chain D from PDB  Type:PROTEIN  Length:565
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhhh...eeee.....hhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh...eeeeeee.hhhhh...............hhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhh..eeeeee......ee.ee.hhhhhhh....hhhhhhhhhhhhhhhh.....eeeee........hhhhhhhhhhhhh.eeeee.hhh.........eeeeehhhhh..hhhhhhhhh.eeeee....................eeee...eeee..eeee..hhhhhhhhhhhhh...hhhhhhhhhhh................hhhhhhhhhhhhh...eeeee..hhhhhhhhh.......eee.........hhhhhhhhhhhhh...eeeeeeehhhhhhhh.hhhhhhhh....eeeeee...hhhhhhhhhhhhhh....hhhhhhhhhhh.........eeeee.hhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zp1 D   2 SYTVGTYLAERLVQIGLKHHFAVAGDYNLVLLDNLLLNKNMEQVYCCNELNCGFSAEGYARAKGAAAAVVTYSVGALSAFDAIGGAYAENLPVILISGAPNNNDHAAGHVLHHALGKTDYHYQLEMAKNITAAAEAIYTPEEAPAKIDHVIKTALREKKPVYLEIACNIASMPCAAPGPASALFNDEASDEASLNAAVEETLKFIANRDKVAVLVGSKLRAAGAEEAAVKFADALGGAVATMAAAKSFFPEENPHYIGTSWGEVSYPGVEKTMKEADAVIALAPVFNDYSTTGWTDIPDPKKLVLAEPRSVVVNGIRFPSVHLKDYLTRLAQKVSKKTGALDFFKSLNAGELKKAAPADPSAPLVNAEIARQVEALLTPNTTVIAETGDSWFNAQRMKLPNGARVEYEMQWGHIGWSVPAAFGYAVGAPERRNILMVGDGSFQLTAQEVAQMVRLKLPVIIFLINNYGYTIAVMIHDGPYNNIKNWDYAGLMEVFNGNGGYDSGAGKGLKAKTGGELAEAIKVALANTDGPTLIECFIGREDCTEELVKWGKRVAAANSRKPVNK 566
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 4ZP1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZP1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZP1)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        PDC_ZYMMO | P06672: 1zpd 2wva 2wvg 2wvh 3oe1

(-) Related Entries Specified in the PDB File

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