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(-) Description

Title :  CRYSTAL STRUCTURE OF A NOVEL PYRUVATE DECARBOXYLASE
 
Authors :  S. S. Cha, C. S. Jeong, Y. J. An
Date :  04 May 10  (Deposition) - 18 May 11  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Frsa, Fermentation/Respiration Switch Protein, Hydrolase Activator, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Lee, C. S. Jeong, Y. J. An, H. J. Lee, S. J. Park, Y. J. Seok, P. Kim, J. H. Lee, K. H. Lee, S. S. Cha
Frsa Functions As A Cofactor-Independent Decarboxylase To Control Metabolic Flux.
Nat. Chem. Biol. V. 7 434 2011
PubMed-ID: 21623357  |  Reference-DOI: 10.1038/NCHEMBIO.589

(-) Compounds

Molecule 1 - UPF0255 PROTEIN VV1_0328
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FRSA, VV1_0328
    Organism Scientific: VIBRIO VULNIFICUS
    Organism Taxid: 672
    Strain: M06-24/0
    Synonym: FRSA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2SO45Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:79 , SER A:80 , HIS A:94 , HOH A:521 , HOH A:551BINDING SITE FOR RESIDUE SO4 A 416
02AC2SOFTWAREGLY A:201 , LEU A:202 , ARG A:272 , PHE A:273 , TYR A:316BINDING SITE FOR RESIDUE EDO A 417
03AC3SOFTWARETYR A:93 , THR A:103 , MET A:107 , EDO A:419 , HOH A:543 , GLN B:110 , SER B:155 , HOH B:504BINDING SITE FOR RESIDUE EDO A 418
04AC4SOFTWARETYR A:93 , THR A:103 , LEU A:145 , LEU A:152 , EDO A:418 , SER B:155BINDING SITE FOR RESIDUE EDO A 419
05AC5SOFTWARELEU A:125 , GLU A:159 , LYS A:162 , LYS A:163 , HOH A:554 , GLY B:92 , TYR B:93BINDING SITE FOR RESIDUE EDO A 420
06AC6SOFTWAREPHE A:46 , SER A:47 , TRP A:48 , HOH A:562BINDING SITE FOR RESIDUE EDO A 421
07AC7SOFTWAREPHE A:283 , GLY A:347 , PHE A:348 , ARG A:352BINDING SITE FOR RESIDUE EDO A 422
08AC8SOFTWARESER A:77 , LYS A:78 , HIS A:79 , SER A:95 , GLY A:96 , HOH A:508 , HOH A:571BINDING SITE FOR RESIDUE EDO A 423
09AC9SOFTWARELYS A:21 , GLU A:22 , THR A:23 , ARG A:50 , ASN A:97 , TRP A:98 , ALA A:99 , LEU A:145 , HOH A:505 , HOH A:545BINDING SITE FOR RESIDUE EDO A 424
10BC1SOFTWAREHIS B:79 , SER B:80 , HOH B:452 , HOH B:453BINDING SITE FOR RESIDUE SO4 B 416
11BC2SOFTWAREGLY B:201 , LEU B:202 , ASP B:203 , ARG B:272 , PHE B:273 , HOH B:522BINDING SITE FOR RESIDUE SO4 B 417
12BC3SOFTWARELYS B:179 , LYS B:237 , HOH B:549BINDING SITE FOR RESIDUE SO4 B 418
13BC4SOFTWAREHIS B:216 , HIS B:220 , ILE B:222 , ILE B:406 , LYS B:407 , GLU B:410BINDING SITE FOR RESIDUE SO4 B 419
14BC5SOFTWAREGLU B:22 , THR B:23 , ARG B:50 , ASN B:97 , ALA B:99 , LEU B:145 , HOH B:438 , HOH B:456 , HOH B:463 , HOH B:565BINDING SITE FOR RESIDUE EDO B 420
15BC6SOFTWAREVAL B:58 , GLY B:61 , VAL B:62 , ASP B:63 , ARG B:211 , HOH B:449 , HOH B:557BINDING SITE FOR RESIDUE EDO B 421

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:137 -Pro A:138
2Tyr B:137 -Pro B:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MVE)

(-) 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:396
 aligned with Y328_VIBVU | Q8DF91 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:396
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409      
           Y328_VIBVU    20 AKETSALTQYMPTSQSLLDEIKEKNGFSWYRNLRRLQWVWQGVDPIEQEQVLARIASSKHSRTDEQWLDTVMGYHSGNWAYEWTRLGMEHQKRAGEMTNEAASEALFSASLCYSIAGYPHLKSDNLAIQAQVLANSAYLEAAKKSKYIIKQLEIPFEKGKITAHLHLTNTDKPHPVVIVSAGLDSLQTDMWRLFRDHLAKHDIAMLTVDMPSVGYSSKYPLTEDYSRLHQAVLNELFSIPYVDHHRVGLIGFRFGGNAMVRLSFLEQEKIKACVILGAPIHDIFASPQKLQQMPKMYLDVLASRLGKSVVDIYSLSGQMAAWSLKVQGFLSSRKTKVPILAMSLEGDPVSPYSDNQMVAFFSTYGKAKKISSKTITQGYEQSLDLAIKWLEDELLR 415
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh...hhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeeee......eeeeeee.....hhhhhhhhhhhhhhhhh.eeeee....hhhhh........hhhhhhhhhhhhhh..eeeeeeeeeeehhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhh...............eeeeee......hhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mve A  20 AKETSALTQYMPTSQSLLDEIKEKNGFSWYRNLRRLQWVWQGVDPIEQEQVLARIASSKHSRTDEQWLDTVMGYHSGNWAYEWTRLGMEHQKRAGEMTNEAASEALFSASLCYSIAGYPHLKSDNLAIQAQVLANSAYLEAAKKSKYIIKQLEIPFEKGKITAHLHLTNTDKPHPVVIVSAGLDSLQTDMWRLFRDHLAKHDIAMLTVDMPSVGYSSKYPLTEDYSRLHQAVLNELFSIPYVDHHRVGLIGFRFGGNAMVRLSFLEQEKIKACVILGAPIHDIFASPQKLQQMPKMYLDVLASRLGKSVVDIYSLSGQMAAWSLKVQGFLSSRKTKVPILAMSLEGDPVSPYSDNQMVAFFSTYGKAKKISSKTITQGYEQSLDLAIKWLEDELLR 415
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409      


Chain B from PDB  Type:PROTEIN  Length:395
 aligned with Y328_VIBVU | Q8DF91 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:395
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410     
           Y328_VIBVU    21 KETSALTQYMPTSQSLLDEIKEKNGFSWYRNLRRLQWVWQGVDPIEQEQVLARIASSKHSRTDEQWLDTVMGYHSGNWAYEWTRLGMEHQKRAGEMTNEAASEALFSASLCYSIAGYPHLKSDNLAIQAQVLANSAYLEAAKKSKYIIKQLEIPFEKGKITAHLHLTNTDKPHPVVIVSAGLDSLQTDMWRLFRDHLAKHDIAMLTVDMPSVGYSSKYPLTEDYSRLHQAVLNELFSIPYVDHHRVGLIGFRFGGNAMVRLSFLEQEKIKACVILGAPIHDIFASPQKLQQMPKMYLDVLASRLGKSVVDIYSLSGQMAAWSLKVQGFLSSRKTKVPILAMSLEGDPVSPYSDNQMVAFFSTYGKAKKISSKTITQGYEQSLDLAIKWLEDELLR 415
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) DUF1100-3mveB01 B:21-414                                                                                                                                                                                                                                                                                                                                                                                  - Pfam domains (1)
           Pfam domains (2) DUF1100-3mveB02 B:21-414                                                                                                                                                                                                                                                                                                                                                                                  - Pfam domains (2)
         Sec.struct. author .hhhhh.eehhhhhhhhhhhhhhhh.......hhhhhhhh..hhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeee......eeeeeee.....hhhhhhhhhhhhhhhhh.eeeee....hhhhh........hhhhhhhhhhhhhh..eeeeeeeeeeehhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhh..hhhhhhhhhhhh...eehhhhhhhhhhhhh...............eeeeee......hhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mve B  21 KETSALTQYMPTSQSLLDEIKEKNGFSWYRNLRRLQWVWQGVDPIEQEQVLARIASSKHSRTDEQWLDTVMGYHSGNWAYEWTRLGMEHQKRAGEMTNEAASEALFSASLCYSIAGYPHLKSDNLAIQAQVLANSAYLEAAKKSKYIIKQLEIPFEKGKITAHLHLTNTDKPHPVVIVSAGLDSLQTDMWRLFRDHLAKHDIAMLTVDMPSVGYSSKYPLTEDYSRLHQAVLNELFSIPYVDHHRVGLIGFRFGGNAMVRLSFLEQEKIKACVILGAPIHDIFASPQKLQQMPKMYLDVLASRLGKSVVDIYSLSGQMAAWSLKVQGFLSSRKTKVPILAMSLEGDPVSPYSDNQMVAFFSTYGKAKKISSKTITQGYEQSLDLAIKWLEDELLR 415
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410
   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 3MVE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: AB_hydrolase (347)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3MVE)

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  Cis Peptide Bonds
    Tyr A:137 - Pro A:138   [ RasMol ]  
    Tyr B:137 - Pro B:138   [ RasMol ]  
 

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 Related Entries

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UniProtKB/Swiss-Prot
        Y328_VIBVU | Q8DF91: 3our

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