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(-) Description

Title :  CRYSTAL STRUCTURE OF PDUA WITH EDGE MUTATION K26A AND PORE MUTATION S40H
 
Authors :  A. H. Pang, M. R. Sawaya, T. O. Yeates
Date :  30 May 14  (Deposition) - 18 Feb 15  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I
Biol. Unit 1:  A,B,C,D,E,F  (1x)
Biol. Unit 2:  G,H,I  (2x)
Keywords :  Bmc Domain, Structural Protein, Potassium, Glycerol, 1-2 Propanediol, Tartaric Acid, Sulfate Ion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chowdhury, S. Chun, A. Pang, M. R. Sawaya, S. Sinha, T. O. Yeates, T. A. Bobik
Selective Molecular Transport Through The Protein Shell Of Bacterial Microcompartment Organelle.
Proc. Natl. Acad. Sci. Usa V. 112 2990 2015
PubMed-ID: 25713376  |  Reference-DOI: 10.1073/PNAS.1423672112

(-) Compounds

Molecule 1 - PROPANEDIOL UTILIZATION PROTEIN PDUA
    Chains: A, B, C, D, E, F, G, H, I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PDUA, STM2038
    Mutation: YES
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2 / SGSC1412 / ATCC 700720

 Structural Features

(-) Chains, Units

  123456789
Asymmetric Unit : ABCDEFGHI
Biological Unit 1 (1x): ABCDEF   
Biological Unit 2 (2x):       GHI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 28)

Asymmetric Unit (5, 28)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2K1Ligand/IonPOTASSIUM ION
3PGO3Ligand/IonS-1,2-PROPANEDIOL
4SO413Ligand/IonSULFATE ION
5TAR3Ligand/IonD(-)-TARTARIC ACID
Biological Unit 1 (4, 20)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2K-1Ligand/IonPOTASSIUM ION
3PGO2Ligand/IonS-1,2-PROPANEDIOL
4SO410Ligand/IonSULFATE ION
5TAR2Ligand/IonD(-)-TARTARIC ACID
Biological Unit 2 (4, 14)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2K-1Ligand/IonPOTASSIUM ION
3PGO2Ligand/IonS-1,2-PROPANEDIOL
4SO46Ligand/IonSULFATE ION
5TAR2Ligand/IonD(-)-TARTARIC ACID

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:38 , HOH A:240 , SO4 C:101 , LYS F:37 , GLY F:39BINDING SITE FOR RESIDUE PGO A 101
02AC2SOFTWAREARG A:48 , HIS A:81 , ASP A:83 , VAL A:84 , GLU A:85BINDING SITE FOR RESIDUE SO4 A 102
03AC3SOFTWAREHIS A:40 , HIS B:40 , HIS C:40 , HIS D:40 , TAR D:101 , HIS E:40 , HIS F:40BINDING SITE FOR RESIDUE SO4 A 103
04AC4SOFTWARELYS A:12 , HIS A:40 , LYS A:72 , HOH A:236 , LYS F:12 , GOL F:102 , GOL F:103BINDING SITE FOR RESIDUE SO4 A 104
05AC5SOFTWAREGLU A:36 , PRO A:89 , TYR F:35 , LYS F:37BINDING SITE FOR RESIDUE SO4 A 105
06AC6SOFTWAREHOH E:209 , HOH I:220BINDING SITE FOR RESIDUE K B 101
07AC7SOFTWARELYS B:12 , HIS B:40 , LYS B:72 , LYS D:12BINDING SITE FOR RESIDUE GOL B 102
08AC8SOFTWARELYS B:37 , HOH B:218 , HOH B:239 , LYS F:37BINDING SITE FOR RESIDUE SO4 B 103
09AC9SOFTWAREPGO A:101 , HOH A:240 , ILE B:38 , LYS C:37 , GLY D:39BINDING SITE FOR RESIDUE SO4 C 101
10BC1SOFTWAREMET B:31 , LEU B:32 , THR F:82BINDING SITE FOR RESIDUE SO4 B 104
11BC2SOFTWAREHOH A:240 , LYS C:37 , GLY C:39 , ILE D:38 , SO4 E:103 , SO4 F:101BINDING SITE FOR RESIDUE PGO C 102
12BC3SOFTWAREGLY A:39 , HIS A:40 , SO4 A:103 , HOH A:207 , HOH A:240 , GLY B:39 , HIS B:40 , GLY C:39 , HIS C:40 , GLY D:39 , HIS D:40 , HOH D:205 , HOH D:232 , GLY E:39 , HIS E:40 , GLY F:39 , HIS F:40BINDING SITE FOR RESIDUE TAR D 101
13BC4SOFTWARELYS C:12 , LYS D:12 , HIS D:40 , LYS D:72 , GOL F:102BINDING SITE FOR RESIDUE TAR D 102
14BC5SOFTWARETYR D:35 , GLU D:36BINDING SITE FOR RESIDUE GOL D 103
15BC6SOFTWAREARG D:48 , ASP D:83 , VAL D:84 , GLU D:85BINDING SITE FOR RESIDUE SO4 D 104
16BC7SOFTWAREARG B:66 , ASN B:67 , GLY B:69 , ALA E:26 , SER E:27 , ALA E:28BINDING SITE FOR RESIDUE GOL E 101
17BC8SOFTWARELYS A:12 , LYS E:12 , HIS E:40 , LYS E:72BINDING SITE FOR RESIDUE GOL E 102
18BC9SOFTWARELYS C:37 , PGO C:102 , HOH C:228 , LYS E:37BINDING SITE FOR RESIDUE SO4 E 103
19CC1SOFTWAREPGO C:102 , HOH D:232 , ILE E:38 , LYS F:37BINDING SITE FOR RESIDUE SO4 F 101
20CC2SOFTWAREHIS A:40 , SO4 A:104 , HOH A:236 , TAR D:102 , HIS F:40BINDING SITE FOR RESIDUE GOL F 102
21CC3SOFTWARELYS A:72 , SO4 A:104 , LYS F:12BINDING SITE FOR RESIDUE GOL F 103
22CC4SOFTWAREGLY G:39 , HIS G:40 , GLY H:39 , HIS H:40 , SO4 H:102 , HOH H:206 , GLY I:39 , HIS I:40BINDING SITE FOR RESIDUE TAR G 101
23CC5SOFTWAREHOH A:229 , ALA G:56 , ASP G:59 , ALA G:60BINDING SITE FOR RESIDUE GOL G 102
24CC6SOFTWARELYS G:12 , HIS G:40 , LYS G:72 , LYS H:12BINDING SITE FOR RESIDUE SO4 G 103
25CC7SOFTWAREARG H:48 , HIS H:81 , VAL H:84 , GLU H:85BINDING SITE FOR RESIDUE GOL H 101
26CC8SOFTWAREHIS G:40 , TAR G:101 , HIS H:40 , HOH H:226 , HIS I:40BINDING SITE FOR RESIDUE SO4 H 102
27CC9SOFTWAREGLU H:36 , LYS H:37 , PRO H:89 , GLY H:91 , LYS I:37BINDING SITE FOR RESIDUE SO4 H 103
28DC1SOFTWARELYS G:12 , LYS I:12 , HIS I:40 , LYS I:72BINDING SITE FOR RESIDUE PGO I 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QIF)

(-) 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:91
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeehhhhhhhhhhhhh....eeeeeeeeee..eeeeeeeeehhhhhhhhhhhhhhhhh..eeeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  4qif A  2 QQEALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGHGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILPKGI 92
                                    11        21        31        41        51        61        71        81        91 


Chain B from PDB  Type:PROTEIN  Length:86
                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhh....eeeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhh...eeeeeeee...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  4qif B  4 EALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGHGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILP 89
                                    13        23        33        43        53        63        73        83      


Chain C from PDB  Type:PROTEIN  Length:90
                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhhhhh.eeeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhh..eeeeeeee.....hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                  4qif C  4 EALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGHGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILPKGIS 93
                                    13        23        33        43        53        63        73        83        93


Chain D from PDB  Type:PROTEIN  Length:88
                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeehhhhhhhhhhhhhhhh..eeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhh..eeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                  4qif D  3 QEALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGHGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILPK 90
                                    12        22        32        42        52        62        72        82        


Chain E from PDB  Type:PROTEIN  Length:86
                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhhhhhhhh.....eeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhh...eeeeeeee.....hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  4qif E  3 QEALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGHGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKIL 88
                                    12        22        32        42        52        62        72        82      


Chain F from PDB  Type:PROTEIN  Length:91
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhh..eeeeeeee.....hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  4qif F  3 QEALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGHGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILPKGIS 93
                                    12        22        32        42        52        62        72        82        92 


Chain G from PDB  Type:PROTEIN  Length:84
                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhhhhh..eeeeeee....eeeeeeeehhhhhhhhhhhhhhhhhh..eeeeeeee....hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  4qif G  4 EALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGHGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKI 87
                                    13        23        33        43        53        63        73        83    


Chain H from PDB  Type:PROTEIN  Length:91
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeehhhhhhhhhhhhhhhh..eeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhheeeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  4qif H  1 TQQEALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGHGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILPKG 91
                                    10        20        30        40        50        60        70        80        90 


Chain I from PDB  Type:PROTEIN  Length:84
                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhh....eeeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhh...eeeeeeee.....hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  4qif I  4 EALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGHGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKI 87
                                    13        23        33        43        53        63        73        83
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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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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  PDUA_SALTY | P0A1C7
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 Related Entries

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

UniProtKB/Swiss-Prot
        PDUA_SALTY | P0A1C7: 3ngk 4ppd 4qie 4qig 4rbt 4rbu 4rbv

(-) Related Entries Specified in the PDB File

3ngk 4p2s 4ppd