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(-) Description

Title :  STRUCTURE OF Y105A MUTANT OF PHAZ7 PHB DEPOLYMERASE
 
Authors :  S. Hermawan, B. Subedi, A. C. Papageorgiou, D. Jendrossek
Date :  26 Jun 13  (Deposition) - 18 Sep 13  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Catalytic Triad, Biopolymer Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Jendrossek, S. Hermawan, B. Subedi, A. C. Papageorgiou
Biochemical Analysis And Structure Determination Of Paucimonas Lemoignei Poly(3-Hydroxybutyrate) (Phb) Depolymerase Phaz7 Muteins Reveal The Phb Binding Site And Details Of Substrate-Enzyme Interactions.
Mol. Microbiol. V. 90 649 2013
PubMed-ID: 24007310  |  Reference-DOI: 10.1111/MMI.12391
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHB DEPOLYMERASE PHAZ7
    Chains: A, B
    EC Number: 3.1.1.75
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Strain: WB800
    Expression System Taxid: 1423
    Fragment: RESIDUES 39-380
    Mutation: YES
    Organism Scientific: PAUCIMONAS LEMOIGNEI
    Organism Taxid: 29443

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1NA3Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:83 , ASP A:84BINDING SITE FOR RESIDUE NA A 501
2AC2SOFTWARECYS A:36 , THR A:37 , HOH A:2605 , HOH A:2606BINDING SITE FOR RESIDUE NA A 601
3AC3SOFTWAREALA B:23 , PRO B:24 , GLY B:25 , HOH B:2616BINDING SITE FOR RESIDUE NA B 501

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:3 -A:11
2A:36 -A:85
3A:171 -A:184
4A:246 -A:255
5A:325 -A:330
6B:3 -B:11
7B:36 -B:85
8B:171 -B:184
9B:246 -B:255
10B:325 -B:330

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4BVJ)

(-) 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:343
 aligned with Q939Q9_PAULE | Q939Q9 from UniProtKB/TrEMBL  Length:380

    Alignment length:343
                                                                                                                                                                                                                                                                                                                                                                               380 
                                    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 | 
         Q939Q9_PAULE    39 LTCGTNSGFVCKGTQTQYAGGFAPGVGYGGFGGGSCTATKTPVIFIHGNGDNAISFDMPPGNVSGYGTPARSVYAELKARGYNDCEIFGVTYLSSSEQGSAQYNYHSSTKYAIIKTFIDKVKAYTGKSQVDIVAHSMGVSMSLATLQYYNNWTSVRKFINLAGGIRGLYSCYYTGYANAAAPTCGSQNYYNSYTFGFFPEGWYYGVWVSNPWTGSGSTNSMRDMPAKRTAVSFYTLSAGFKDQVGCATASFWAGCDSAAKFASTTSNVKAQINVGAGSNATQADYDWADGMPYNAGGGDTTNGVGHFRTKTNTGAIIQRMLLTTCTGLDCAAEYTTGPKAAY-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eee...........eee..........eeee.....hhhhhhh.............hhhhhhhhh......eeee...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh.eeeeeee......hhhhh........hhhhh...............eee..eee...........hhhhhhhhh...eeeeeehhhhh...........hhhhh.........eeeeee............hhhhh................hhhhhhhhhhhhhhhhh..hhhhhhh.......ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bvj A   1 LTCGTNSGFVCKGTQTQYAGGFAPGVGYGGFGGGSCTATKTPVIFIHGNGDNAISFDMPPGNVSGYGTPARSVYAELKARGYNDCEIFGVTYLSSSEQGSAQYNAHSSTKYAIIKTFIDKVKAYTGKSQVDIVAHSMGVSMSLATLQYYNNWTSVRKFINLAGGIRGLYSCYYTGYANAAAPTCGSQNYYNSYTFGFFPEGWYYGVWVSNPWTGSGSTNSMRDMPAKRTAVSFYTLSAGFKDQVGCATASFWAGCDSAAKFASTTSNVKAQINVGAGSNATQADYDWADGMPYNAGGGDTTNGVGHFRTKTNTGAIIQRMLLTTCTGLDCAAEYTTGPKAAYN 343
                                    10        20        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   


Chain B from PDB  Type:PROTEIN  Length:343
 aligned with Q939Q9_PAULE | Q939Q9 from UniProtKB/TrEMBL  Length:380

    Alignment length:343
                                                                                                                                                                                                                                                                                                                                                                               380 
                                    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 | 
         Q939Q9_PAULE    39 LTCGTNSGFVCKGTQTQYAGGFAPGVGYGGFGGGSCTATKTPVIFIHGNGDNAISFDMPPGNVSGYGTPARSVYAELKARGYNDCEIFGVTYLSSSEQGSAQYNYHSSTKYAIIKTFIDKVKAYTGKSQVDIVAHSMGVSMSLATLQYYNNWTSVRKFINLAGGIRGLYSCYYTGYANAAAPTCGSQNYYNSYTFGFFPEGWYYGVWVSNPWTGSGSTNSMRDMPAKRTAVSFYTLSAGFKDQVGCATASFWAGCDSAAKFASTTSNVKAQINVGAGSNATQADYDWADGMPYNAGGGDTTNGVGHFRTKTNTGAIIQRMLLTTCTGLDCAAEYTTGPKAAY-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eee...........eee..........eeee.....hhhhhhh.............hhhhhhhhh......eeee...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh.eeeeeee......hhhhh........hhhhh...............eee..eee...........hhhhhhhhh...eeeeeehhhhhhhhhh......hhhhh.........eeeeee............hhhhh................hhhhhhhhhhhhhhhhh..hhhhhhh.......ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bvj B   1 LTCGTNSGFVCKGTQTQYAGGFAPGVGYGGFGGGSCTATKTPVIFIHGNGDNAISFDMPPGNVSGYGTPARSVYAELKARGYNDCEIFGVTYLSSSEQGSAQYNAHSSTKYAIIKTFIDKVKAYTGKSQVDIVAHSMGVSMSLATLQYYNNWTSVRKFINLAGGIRGLYSCYYTGYANAAAPTCGSQNYYNSYTFGFFPEGWYYGVWVSNPWTGSGSTNSMRDMPAKRTAVSFYTLSAGFKDQVGCATASFWAGCDSAAKFASTTSNVKAQINVGAGSNATQADYDWADGMPYNAGGGDTTNGVGHFRTKTNTGAIIQRMLLTTCTGLDCAAEYTTGPKAAYN 343
                                    10        20        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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4BVJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q939Q9_PAULE | Q939Q9)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.

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  3.1.1.75
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q939Q9_PAULE | Q939Q9: 5mlx 5mly
UniProtKB/TrEMBL
        Q939Q9_PAULE | Q939Q9: 2vtv 2x5x 2x76 4brs 4btv 4bvk 4bvl 4bym

(-) Related Entries Specified in the PDB File

4btv STRUCTURE OF PHAZ7 PHB DEPOLYMERASE IN COMPLEX WITH 3HB TRIMER
4bvk STRUCTURE OF Y190E MUTANT OF PHAZ7 PHB DEPOLYMERASE
4bvl STRUCTURE OF 202-208 DELETION MUTANT OF PHAZ7 PHB DEPOLYMERASE