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Title :   CRYSTAL STRUCTURE OF PUTATIVE GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE (NP_812074.1) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.35 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   25 Jun 09 (Deposition) - 21 Jul 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.35

Chains :   Asym./Biol. Unit : A

Keywords :   Np_812074. 1, Putative Glycerophosphoryl Diester Phosphodiesterase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Glycerophosphoryl Diester Phosphodiesterase (Np_812074. 1) From Bacteroides Thetaiotaomicron Vpi-5482 At 1. 35 A Resolution
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 26)

Sites (21, 21)

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:51 , SER A:52 , ALA A:53 , ASP A:117 , LYS A:118 , HOH A:402 , HOH A:524	BINDING SITE FOR RESIDUE ACT A 1
02	AC2	SOFTWARE	THR A:123 , ASN A:124 , TYR A:125	BINDING SITE FOR RESIDUE ACT A 2
03	AC3	SOFTWARE	EDO A:5 , THR A:58 , HOH A:382 , HOH A:421	BINDING SITE FOR RESIDUE EDO A 3
04	AC4	SOFTWARE	LYS A:161 , LEU A:198 , PRO A:229 , HOH A:318 , HOH A:438 , HOH A:574	BINDING SITE FOR RESIDUE EDO A 4
05	AC5	SOFTWARE	EDO A:3 , GLU A:132 , THR A:136 , ASP A:225 , HOH A:479	BINDING SITE FOR RESIDUE EDO A 5
06	AC6	SOFTWARE	LEU A:42 , ASP A:70 , HIS A:300 , ASN A:301 , HOH A:341 , HOH A:455 , HOH A:494	BINDING SITE FOR RESIDUE EDO A 6
07	AC7	SOFTWARE	EDO A:16 , TYR A:289 , ASP A:292 , TYR A:293 , LYS A:296 , HOH A:583	BINDING SITE FOR RESIDUE EDO A 7
08	AC8	SOFTWARE	GLY A:173 , VAL A:195 , ASP A:197 , HOH A:572	BINDING SITE FOR RESIDUE EDO A 8
09	AC9	SOFTWARE	ASN A:39 , ARG A:280 , TRP A:299 , HOH A:303 , HOH A:613	BINDING SITE FOR RESIDUE EDO A 9
10	BC1	SOFTWARE	EDO A:11 , ARG A:47 , GLU A:55 , LYS A:80 , ARG A:94 , HOH A:468 , HOH A:490	BINDING SITE FOR RESIDUE EDO A 10
11	BC2	SOFTWARE	EDO A:10 , HOH A:22 , PRO A:54 , GLU A:55 , THR A:95 , LYS A:116 , ASP A:117 , LYS A:118	BINDING SITE FOR RESIDUE EDO A 11
12	BC3	SOFTWARE	GLY A:255 , HIS A:257 , HOH A:495	BINDING SITE FOR RESIDUE EDO A 12
13	BC4	SOFTWARE	PRO A:36 , LYS A:37 , LEU A:191 , HOH A:503 , HOH A:592	BINDING SITE FOR RESIDUE EDO A 13
14	BC5	SOFTWARE	PRO A:36 , LYS A:37 , SER A:38 , PHE A:239 , LYS A:240 , ARG A:280 , HOH A:358 , HOH A:440 , HOH A:533	BINDING SITE FOR RESIDUE EDO A 14
15	BC6	SOFTWARE	LYS A:99 , GLY A:100 , TRP A:105 , ASN A:260 , LEU A:263 , THR A:264 , HOH A:385 , HOH A:493 , HOH A:612	BINDING SITE FOR RESIDUE EDO A 15
16	BC7	SOFTWARE	EDO A:7 , LYS A:205 , TYR A:289	BINDING SITE FOR RESIDUE EDO A 16
17	BC8	SOFTWARE	ASP A:197 , ILE A:222 , SER A:224 , SER A:252 , HOH A:373 , HOH A:513	BINDING SITE FOR RESIDUE EDO A 17
18	BC9	SOFTWARE	LYS A:30 , ASN A:166 , LEU A:191 , HOH A:372 , HOH A:410	BINDING SITE FOR RESIDUE EDO A 18
19	CC1	SOFTWARE	GLN A:77 , LYS A:78 , LYS A:103 , HOH A:474 , HOH A:593	BINDING SITE FOR RESIDUE EDO A 19
20	CC2	SOFTWARE	ASN A:90 , THR A:91 , HOH A:492	BINDING SITE FOR RESIDUE EDO A 20
21	CC3	SOFTWARE	LYS A:171 , GLU A:220 , ASN A:247 , HOH A:353 , HOH A:406 , HOH A:508 , HOH A:555	BINDING SITE FOR RESIDUE PEG A 21

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:278
 aligned with Q8A2Z3_BACTN | Q8A2Z3 from UniProtKB/TrEMBL  Length:301

    Alignment length:278
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293        
         Q8A2Z3_BACTN    24 QHVETIKNTFLNPKSNKVLVVAHRGNWRSAPENSTAAIDSAIAMKVDIVEIDIQKTKDGQLILMHDNTLDRTTTGKGEIKNWTLADIKKLKLKDKDGKVTNYVVPTLEEALLTAKGKIMVNLDKAYDIFDDVYAILEKTETQNQVIMKGGQPIETVKREFGSYLDKVLYMPVIDLGNKEAEKIITDYLKELRPAAFEIIYSDPKNPLPPKIKQLLFKKSLIWYNTLWGSLAGNHDDNLALTDPEKSYGYLIEQLGARILQTDQPAYLLDYLRKKGWHN 301
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.......eeeee..........hhhhhhhhhhh...eeeeeeee.....eee..............hhhhhhhhhhh.................hhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhh...eeeee.......hhhhhhhhhh...eeeee..hhhhh...hhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i10 A   0 GHVETIKNTFLNPKSNKVLVVAHRGNWRSAPENSTAAIDSAIAmKVDIVEIDIQKTKDGQLILmHDNTLDRTTTGKGEIKNWTLADIKKLKLKDKDGKVTNYVVPTLEEALLTAKGKImVNLDKAYDIFDDVYAILEKTETQNQVImKGGQPIETVKREFGSYLDKVLYmPVIDLGNKEAEKIITDYLKELRPAAFEIIYSDPKNPLPPKIKQLLFKKSLIWYNTLWGSLAGNHDDNLALTDPEKSYGYLIEQLGARILQTDQPAYLLDYLRKKGWHN 301
                            ||      33        43        53        63   |    73        83   |    93       103       113       123       133       143       153       163      |173       183       193       203       213       223       233       243       253       263       273       283       293        
                            ||                                        67-MSE              87-MSE                                                142-MSE                     170-MSE                193-MSE                                                                                                        
                            0|                                                                                                                                                                                                                                                                                    
                            25

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Classification and Annotation

SCOP Domains (0, 0)

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Pfam Domains (0, 0)

Gene Ontology (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q8A2Z3_BACTN | Q8A2Z3)

molecular function
	GO:0008889	glycerophosphodiester phosphodiesterase activity	Catalysis of the reaction: a glycerophosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate.
	GO:0008081	phosphoric diester hydrolase activity	Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
biological process
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.

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