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(-) Description

Title :  THE CRYSTAL STRUCTURE OF PHAZ7 AT ATOMIC (1.2 ANGSTROM) RESOLUTION REVEALS DETAILS OF THE ACTIVE SITE AND SUGGESTS A SUBSTRATE BINDING MODE
 
Authors :  S. Wakadkar, S. Hermawan, D. Jendrossek, A. C. Papageorgiou
Date :  11 Feb 10  (Deposition) - 09 Jun 10  (Release) - 16 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Biopolymers, Oxyanion Hole, Hydrolase, Biodegradation, Catalytic Tria (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Wakadkar, S. Hermawan, D. Jendrossek, A. C. Papageorgiou
The Structure Of Phaz7 At Atomic (1. 2 A) Resolution Reveals Details Of The Active Site And Suggests A Substrate-Binding Mode.
Acta Crystallogr. , Sect. F V. 66 648 2010
PubMed-ID: 20516591  |  Reference-DOI: 10.1107/S174430911001434X

(-) Compounds

Molecule 1 - PHB DEPOLYMERASE PHAZ7
    Chains: A
    Fragment: RESIDUES 39-380
    Organism Scientific: PAUCIMONAS LEMOIGNEI
    Organism Taxid: 29443

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 18)

Asymmetric Unit (5, 18)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2IOD8Ligand/IonIODIDE ION
3NA2Ligand/IonSODIUM ION
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5SO21Ligand/IonSULFUR DIOXIDE
Biological Unit 1 (3, 20)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2IOD16Ligand/IonIODIDE ION
3NA-1Ligand/IonSODIUM ION
4PG42Ligand/IonTETRAETHYLENE GLYCOL
5SO22Ligand/IonSULFUR DIOXIDE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:7 , SER A:35 , NA A:1357BINDING SITE FOR RESIDUE IOD A1343
02AC2SOFTWAREGLY A:25 , HOH A:2032BINDING SITE FOR RESIDUE IOD A1345
03AC3SOFTWAREGLY A:27 , HOH A:2079BINDING SITE FOR RESIDUE IOD A1346
04AC4SOFTWAREARG A:156 , LYS A:157 , ALA A:341 , HOH A:2525BINDING SITE FOR RESIDUE IOD A1347
05AC5SOFTWAREASN A:6 , HOH A:2008BINDING SITE FOR RESIDUE IOD A1348
06AC6SOFTWAREASN A:49 , SER A:136 , MET A:291 , HIS A:306 , PHE A:307 , HOH A:2561BINDING SITE FOR RESIDUE SO2 A1349
07AC7SOFTWARETYR A:105 , TYR A:176 , GLY A:185 , SER A:186 , GLN A:187 , ASN A:188 , HOH A:2267 , HOH A:2372 , HOH A:2562BINDING SITE FOR RESIDUE PG4 A1350
08AC8SOFTWAREGLY A:205BINDING SITE FOR RESIDUE CL A1351
09AC9SOFTWAREMET A:291 , HOH A:2254BINDING SITE FOR RESIDUE CL A1352
10BC1SOFTWAREASN A:294BINDING SITE FOR RESIDUE CL A1353
11BC2SOFTWAREGLY A:65BINDING SITE FOR RESIDUE CL A1354
12BC3SOFTWAREASP A:84BINDING SITE FOR RESIDUE CL A1355
13BC4SOFTWARETYR A:204BINDING SITE FOR RESIDUE CL A1356
14BC5SOFTWARETHR A:5 , LYS A:12 , GLY A:20 , SER A:35 , IOD A:1343 , HOH A:2015BINDING SITE FOR RESIDUE NA A1357
15BC6SOFTWARETYR A:173 , TYR A:204 , SER A:250 , PHE A:251 , HOH A:2498BINDING SITE FOR RESIDUE NA A1358
16BC7SOFTWAREHOH A:2535BINDING SITE FOR RESIDUE IOD A1359
17BC8SOFTWARETHR A:41 , HOH A:2536BINDING SITE FOR RESIDUE IOD A1360

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1A:3 -A:11
2A:36 -A:85
3A:171 -A:184
4A:246 -A:255
5A:325 -A:330

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2X5X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X5X)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 2X5X)

(-) 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:342
 aligned with Q939Q9_PAULE | Q939Q9 from UniProtKB/TrEMBL  Length:380

    Alignment length:342
                                    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 380
               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
                 2x5x A   1 LTCGTNSGFVCKGTQTQYAGGFAPGVGYGGFGGGSCTATKTPVIFIHGNGDNAISFDMPPGNVSGYGTPARSVYAELKARGYNDCEIFGVTYLSSSEQGSAQYNYHSSTKYAIIKTFIDKVKAYTGKSQVDIVAHSMGVSMSLATLQYYNNWTSVRKFINLAGGIRGLYSCYYTGYANAAAPTCGSQNYYNSYTFGFFPEGWYYGVWVSNPWTGSGSTNSMRDMPAKRTAVSFYTLSAGFKDQVGCATASFWAGCDSAAKFASTTSNVKAQINVGAGSNATQADYDWADGMPYNAGGGDTTNGVGHFRTKTNTGAIIQRMLLTTCTGLDCAAEYTTGPKAAY 342
                                    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
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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 2X5X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2X5X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2X5X)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A   (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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 Related Entries

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

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        Q939Q9_PAULE | Q939Q9: 5mlx 5mly
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        Q939Q9_PAULE | Q939Q9: 2vtv 2x76 4brs 4btv 4bvj 4bvk 4bvl 4bym

(-) Related Entries Specified in the PDB File

2vtv PHAZ7 DEPOLYMERASE FROM PAUCIMONAS LEMOIGNEI