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(-) Description

Title :  THE STRUCTURE OF AN OLEISPIRA ANTARCTICA PHOSPHODIESTERASE OLEI02445 IN COMPLEX WITH THE PRODUCT SN-GLYCEROL-3-PHOSPHATE
 
Authors :  A. U. Singer, O. Kagan, E. Evdokimova, M. E. Cuff, A. M. Edwards, A. Joach A. F. Yakunin, A. Savchenko, Midwest Center For Structural Genom (Mcsg)
Date :  25 Feb 11  (Deposition) - 13 Apr 11  (Release) - 13 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B (1x),C (1x)
Keywords :  Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Alpha-Beta Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. U. Singer, O. Kagan, E. Evdokimova, M. E. Cuff, A. M. Edwards, A. Joachimiak, A. F. Yakunin, A. Savchenko
The Structure Of An Oleispira Antarctica Phosphodiesterase Olei02445 In Complex With The Product Sn-Glycerol-3-Phosphate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHODIESTERASE OLEI02445
    Chains: A, B, C, D
    EC Number: 3.1.4.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: OLEI02445
    Organism Scientific: OLEISPIRA ANTARCTICA
    Organism Taxid: 188908

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  B (1x)C (1x) 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 57)

Asymmetric Unit (8, 57)
No.NameCountTypeFull Name
1CL18Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3G3P4Ligand/IonSN-GLYCEROL-3-PHOSPHATE
4MG13Ligand/IonMAGNESIUM ION
5MSE10Mod. Amino AcidSELENOMETHIONINE
6NA7Ligand/IonSODIUM ION
7NI1Ligand/IonNICKEL (II) ION
8PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (4, 9)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3G3P2Ligand/IonSN-GLYCEROL-3-PHOSPHATE
4MG-1Ligand/IonMAGNESIUM ION
5MSE5Mod. Amino AcidSELENOMETHIONINE
6NA-1Ligand/IonSODIUM ION
7NI-1Ligand/IonNICKEL (II) ION
8PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3G3P1Ligand/IonSN-GLYCEROL-3-PHOSPHATE
4MG-1Ligand/IonMAGNESIUM ION
5MSE3Mod. Amino AcidSELENOMETHIONINE
6NA-1Ligand/IonSODIUM ION
7NI-1Ligand/IonNICKEL (II) ION
8PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (45, 45)

Asymmetric Unit (45, 45)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:14 , ARG A:15 , GLU A:41 , ASP A:43 , HIS A:56 , GLU A:116 , PHE A:150 , ASN A:170 , HOH A:265 , HOH A:287 , HOH A:289 , MG A:310 , HOH A:533BINDING SITE FOR RESIDUE G3P A 301
02AC2SOFTWAREGLU A:41 , ASP A:43 , GLU A:116 , HOH A:287 , G3P A:301BINDING SITE FOR RESIDUE MG A 310
03AC3SOFTWAREHOH A:296 , HOH A:333 , HOH A:361 , HOH A:371 , HOH A:579 , HOH C:273BINDING SITE FOR RESIDUE MG A 311
04AC4SOFTWAREHOH A:374 , HOH A:504 , HOH A:605BINDING SITE FOR RESIDUE MG A 252
05AC5SOFTWAREPHE A:197 , LYS D:72BINDING SITE FOR RESIDUE NA A 253
06AC6SOFTWAREGLU A:90 , EDO A:263 , HOH A:353 , HOH B:460BINDING SITE FOR RESIDUE NA A 255
07AC7SOFTWAREGLY A:48 , PRO A:74BINDING SITE FOR RESIDUE NA A 256
08AC8SOFTWARETYR A:59 , SER A:61 , GLY A:68BINDING SITE FOR RESIDUE CL A 257
09AC9SOFTWARETRP A:162 , PRO A:163 , GLU A:164BINDING SITE FOR RESIDUE CL A 258
10BC1SOFTWAREPRO A:9 , GLN A:10 , HOH A:292BINDING SITE FOR RESIDUE CL A 259
11BC2SOFTWAREGLN A:194 , ASN A:218 , ASP A:219 , HOH A:573BINDING SITE FOR RESIDUE CL A 260
12BC3SOFTWAREGLN A:89 , HOH A:504BINDING SITE FOR RESIDUE CL A 261
13BC4SOFTWAREALA A:208 , GLY A:209 , TYR A:210BINDING SITE FOR RESIDUE PEG A 262
14BC5SOFTWAREGLU A:90 , TYR A:91 , NA A:255 , HOH A:664BINDING SITE FOR RESIDUE EDO A 263
15BC6SOFTWAREHIS A:138 , HOH A:378 , HOH A:379 , HIS B:138 , HOH B:342BINDING SITE FOR RESIDUE NI A 264
16BC7SOFTWAREHIS B:14 , ARG B:15 , GLU B:41 , ASP B:43 , HIS B:56 , GLU B:116 , LYS B:118 , PHE B:150 , ASN B:170 , HOH B:268 , HOH B:284 , MG B:310BINDING SITE FOR RESIDUE G3P B 301
17BC8SOFTWAREGLU B:41 , ASP B:43 , GLU B:116 , HOH B:268 , G3P B:301BINDING SITE FOR RESIDUE MG B 310
18BC9SOFTWAREHOH A:334 , HOH A:353 , HOH A:664 , ASP B:204 , HOH B:308 , HOH B:319 , HOH B:386BINDING SITE FOR RESIDUE MG B 311
19CC1SOFTWAREGLU B:164 , HOH B:340 , HOH B:341 , HOH B:600 , HOH B:671BINDING SITE FOR RESIDUE MG B 252
20CC2SOFTWAREASP B:58 , GLU B:121 , HOH B:343BINDING SITE FOR RESIDUE MG B 253
21CC3SOFTWAREPHE B:147 , ALA B:158 , TRP B:162 , ILE B:165 , ARG B:167BINDING SITE FOR RESIDUE NA B 254
22CC4SOFTWARESER B:61 , ASP B:67 , GLY B:68BINDING SITE FOR RESIDUE CL B 255
23CC5SOFTWAREPRO B:9 , GLN B:10BINDING SITE FOR RESIDUE CL B 256
24CC6SOFTWAREGLN B:194 , ASN B:218 , ASP B:219BINDING SITE FOR RESIDUE CL B 257
25CC7SOFTWARESER B:3 , TYR B:5 , HOH B:561 , HOH B:612BINDING SITE FOR RESIDUE CL B 258
26CC8SOFTWAREHOH A:548 , PRO B:52 , THR B:98 , LEU B:99 , LEU B:100BINDING SITE FOR RESIDUE CL B 259
27CC9SOFTWAREASN A:228 , GLN A:229 , LYS B:225BINDING SITE FOR RESIDUE CL B 260
28DC1SOFTWAREGLY B:48 , ASP B:49 , LYS B:72 , PRO B:74BINDING SITE FOR RESIDUE EDO B 261
29DC2SOFTWAREHIS C:14 , ARG C:15 , GLU C:41 , ASP C:43 , HIS C:56 , GLU C:116 , PHE C:150 , ASN C:170 , PHE C:215 , HOH C:267 , HOH C:270 , MG C:310 , HOH C:451 , HOH C:900 , HOH C:925BINDING SITE FOR RESIDUE G3P C 301
30DC3SOFTWAREGLU C:41 , ASP C:43 , GLU C:116 , HOH C:270 , G3P C:301BINDING SITE FOR RESIDUE MG C 310
31DC4SOFTWARESER C:61 , THR C:64 , HOH C:314 , HOH C:332 , HOH C:545 , HOH C:556BINDING SITE FOR RESIDUE MG C 311
32DC5SOFTWAREHOH C:360 , HOH C:723 , HOH C:790BINDING SITE FOR RESIDUE NA C 252
33DC6SOFTWARETYR C:59 , SER C:61 , ASP C:67 , GLY C:68BINDING SITE FOR RESIDUE CL C 253
34DC7SOFTWAREGLN C:194 , ASN C:218 , ASP C:219 , HOH C:617BINDING SITE FOR RESIDUE CL C 254
35DC8SOFTWAREPRO C:9 , GLN C:10 , HOH C:284BINDING SITE FOR RESIDUE CL C 255
36DC9SOFTWARETRP C:39 , PRO C:144 , HOH C:601 , HOH C:610 , HOH C:645BINDING SITE FOR RESIDUE CL C 256
37EC1SOFTWAREGLN C:137 , TRP C:139 , HOH C:338BINDING SITE FOR RESIDUE PEG C 258
38EC2SOFTWAREHIS D:14 , ARG D:15 , GLU D:41 , ASP D:43 , HIS D:56 , GLU D:116 , PHE D:150 , ASN D:170 , PHE D:215 , HOH D:262 , HOH D:263 , MG D:310 , HOH D:319 , HOH D:481 , HOH D:817BINDING SITE FOR RESIDUE G3P D 301
39EC3SOFTWAREGLU D:41 , ASP D:43 , GLU D:116 , HOH D:263 , G3P D:301BINDING SITE FOR RESIDUE MG D 310
40EC4SOFTWARESER D:61 , THR D:64 , HOH D:296 , HOH D:304 , HOH D:407 , HOH D:841BINDING SITE FOR RESIDUE MG D 311
41EC5SOFTWAREHOH C:845 , HOH C:860 , HOH D:651 , HOH D:902 , HOH D:903BINDING SITE FOR RESIDUE MG D 252
42EC6SOFTWAREHOH D:329 , HOH D:354 , HOH D:387 , HOH D:449BINDING SITE FOR RESIDUE MG D 253
43EC7SOFTWAREALA D:166 , ARG D:167 , ASP D:186 , ALA D:188 , HOH D:351BINDING SITE FOR RESIDUE NA D 254
44EC8SOFTWAREGLN D:35 , TYR D:238 , PRO D:239 , GLN D:240BINDING SITE FOR RESIDUE CL D 255
45EC9SOFTWAREGLN D:194 , ASN D:218 , ASP D:219BINDING SITE FOR RESIDUE CL D 256

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:215 -Thr A:216
2Phe B:215 -Thr B:216
3Phe C:215 -Thr C:216
4Phe D:215 -Thr D:216

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QVQ)

(-) 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:251
                                                                                                                                                                                                                                                                                           
               SCOP domains d3qvqa_ A: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..eeee..........hhhhhhhhhhh...eeeeeeee.....eee..............hhhhhhhhhhh........hhhhh.....hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh....eeee......hhhhhhhhhh..eeeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhh...eeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qvq A   0 GmQSAYSFLPQVIAHRGSSGQAPENTLASLHLAGQQGIKWVEIDVmLSGDGIPVIFHDDYLSRTTDGDGLIYKTPLAELKQLDAGSWKGQEYQQETIPTLLEAIEVISQYGmGLNLELKPCEGLEEETIAASVEVLKQHWPQDLPLLFSSFNYFALVSAKALWPEIARGYNVSAIPSAWQERLEHLDCAGLHIHQSFFDVQQVSDIKAAGYKVLAFTINDESLALKLYNQGLDAVFSDYPQKIQSAIDSHI 250
                             |       9        19        29        39     |  49        59        69        79        89        99       109 |     119       129       139       149       159       169       179       189       199       209       219       229       239       249 
                             |                                          45-MSE                                                           111-MSE                                                                                                                                       
                             1-MSE                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains d3qvqb_ B: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..eeee..........hhhhhhhhhhh...eeeeeeee.....eee..............hhhhhhhhhhh........hhhhh.....hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh...eeeee......hhhhhhhhhh..eeeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhh...eeee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qvq B   0 GmQSAYSFLPQVIAHRGSSGQAPENTLASLHLAGQQGIKWVEIDVmLSGDGIPVIFHDDYLSRTTDGDGLIYKTPLAELKQLDAGSWKGQEYQQETIPTLLEAIEVISQYGmGLNLELKPCEGLEEETIAASVEVLKQHWPQDLPLLFSSFNYFALVSAKALWPEIARGYNVSAIPSAWQERLEHLDCAGLHIHQSFFDVQQVSDIKAAGYKVLAFTINDESLALKLYNQGLDAVFSDYPQKIQSAIDSH 249
                             |       9        19        29        39     |  49        59        69        79        89        99       109 |     119       129       139       149       159       169       179       189       199       209       219       229       239       249
                             1-MSE                                      45-MSE                                                           111-MSE                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains d3qvqc_ C: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeee..........hhhhhhhhhhh...eeeeeeee.....eee..............hhhhhhhhhhh........hhhhh.....hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh...eeeee......hhhhhhhhhh..eeeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhh...eeee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qvq C   2 QSAYSFLPQVIAHRGSSGQAPENTLASLHLAGQQGIKWVEIDVmLSGDGIPVIFHDDYLSRTTDGDGLIYKTPLAELKQLDAGSWKGQEYQQETIPTLLEAIEVISQYGmGLNLELKPCEGLEEETIAASVEVLKQHWPQDLPLLFSSFNYFALVSAKALWPEIARGYNVSAIPSAWQERLEHLDCAGLHIHQSFFDVQQVSDIKAAGYKVLAFTINDESLALKLYNQGLDAVFSDYPQKIQSAIDSHIN 251
                                    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
                                                                      45-MSE                                                           111-MSE                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains d3qvqd_ D: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeee..........hhhhhhhhhhh...eeeeeeee.....eee..............hhhhhhhhhhh........hhhhh.....hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh...eeeee......hhhhhhhhhh..eeeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhh...eeee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qvq D   2 QSAYSFLPQVIAHRGSSGQAPENTLASLHLAGQQGIKWVEIDVmLSGDGIPVIFHDDYLSRTTDGDGLIYKTPLAELKQLDAGSWKGQEYQQETIPTLLEAIEVISQYGmGLNLELKPCEGLEEETIAASVEVLKQHWPQDLPLLFSSFNYFALVSAKALWPEIARGYNVSAIPSAWQERLEHLDCAGLHIHQSFFDVQQVSDIKAAGYKVLAFTINDESLALKLYNQGLDAVFSDYPQKIQSAIDS 248
                                    11        21        31        41   |    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
                                                                      45-MSE                                                           111-MSE
   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QVQ)

(-) Gene Ontology  (0, 0)

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

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  3qvq
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