3CH0 - JenaLib

Title :   CRYSTAL STRUCTURE OF GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE (YP_677622.1) FROM CYTOPHAGA HUTCHINSONII ATCC 33406 AT 1.50 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   06 Mar 08 (Deposition) - 18 Mar 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Yp_677622. 1, 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 Glycerophosphoryl Diester Phosphodiesterase (Yp_677622. 1) From Cytophaga Hutchinsonii Atcc 33406 At 1. 50 A Resolution
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 25)

Sites (18, 18)

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:13 , ARG A:14 , GLU A:40 , ASP A:42 , HIS A:55 , GLU A:135 , LYS A:137 , PHE A:175 , LEU A:195 , TRP A:241 , HOH A:300 , HOH A:538 , HOH A:668	BINDING SITE FOR RESIDUE CIT A 272
02	AC2	SOFTWARE	HIS A:60 , HIS A:61 , GLU A:62 , HOH A:544	BINDING SITE FOR RESIDUE EDO A 273
03	AC3	SOFTWARE	TYR A:182 , GLN A:186 , GLU A:197 , ASP A:219 , THR A:221 , HOH A:385 , HOH A:583	BINDING SITE FOR RESIDUE EDO A 274
04	AC4	SOFTWARE	ASP A:219 , TRP A:241 , THR A:242 , HOH A:373 , HOH A:466	BINDING SITE FOR RESIDUE EDO A 275
05	AC5	SOFTWARE	LEU A:206 , LEU A:209 , SER A:210 , PHE A:211 , THR A:212 , HOH A:524	BINDING SITE FOR RESIDUE EDO A 276
06	AC6	SOFTWARE	LYS A:30 , GLU A:92 , ILE A:93 , ASP A:94 , HOH A:330 , HOH A:625	BINDING SITE FOR RESIDUE EDO A 277
07	AC7	SOFTWARE	THR A:242 , ASN A:244 , GLU A:248 , HOH A:364	BINDING SITE FOR RESIDUE EDO A 278
08	AC8	SOFTWARE	ARG A:17 , ARG A:102 , THR A:242 , ASN A:244 , ASP A:263 , HOH A:484 , HOH A:505	BINDING SITE FOR RESIDUE EDO A 279
09	AC9	SOFTWARE	ASP A:155 , ALA A:159 , LYS A:162 , TYR A:187 , LYS A:199 , HOH A:532 , HOH A:617	BINDING SITE FOR RESIDUE EDO A 280
10	BC1	SOFTWARE	ASP A:155 , LYS A:199 , HOH A:459 , HOH A:616	BINDING SITE FOR RESIDUE EDO A 281
11	BC2	SOFTWARE	GLU A:141 , GLU A:250 , THR A:251 , SER A:254 , HOH A:467 , HOH A:570 , HOH A:649 , HOH A:683	BINDING SITE FOR RESIDUE EDO A 282
12	BC3	SOFTWARE	ALA A:26 , HOH A:360 , HOH A:502	BINDING SITE FOR RESIDUE EDO A 283
13	BC4	SOFTWARE	LEU A:19 , LYS A:30 , ASP A:68 , GLY A:69 , LYS A:107 , HOH A:292 , HOH A:378 , HOH A:508	BINDING SITE FOR RESIDUE EDO A 284
14	BC5	SOFTWARE	SER A:7 , GLN A:131 , HOH A:453	BINDING SITE FOR RESIDUE EDO A 285
15	BC6	SOFTWARE	ARG A:102 , PHE A:103 , LYS A:104 , SER A:105 , TYR A:264 , HOH A:418 , HOH A:677	BINDING SITE FOR RESIDUE EDO A 286
16	BC7	SOFTWARE	GLU A:92 , ASP A:94 , HOH A:423 , HOH A:458	BINDING SITE FOR RESIDUE EDO A 287
17	BC8	SOFTWARE	GLU A:207 , LEU A:209 , SER A:210 , HOH A:676	BINDING SITE FOR RESIDUE EDO A 288
18	BC9	SOFTWARE	ARG A:14 , ARG A:17 , HIS A:55 , ARG A:102 , HOH A:300	BINDING SITE FOR RESIDUE GOL A 289

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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:272
 aligned with Q11WD4_CYTH3 | Q11WD4 from UniProtKB/TrEMBL  Length:271

    Alignment length:272
                             1                                                                                                                                                                                                                                                                              
                             |       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       259       269  
         Q11WD4_CYTH3     - -MIQVPASFDIQGHRGCRGLLPENTIAAFTKALLLGVTTLEFDLVISKDNRVVVSHDTFFHHEITMMVDGEDVTEANEKNFNLYAMNYADIKEIDVGMKTHPRFKSQKKVPAVKPLFRELIETAEKLSAKIQYNGEIKSTVEGDNIDHPNIALFCDLVVAEIKKAHITDRFTLQSFDVRALEYMHSQYPDIKLSYLVETKGTLKKQLEKLSFTPAVYSPDVTLVSKKDIDAAHKLGMRVIPWTVNTKEEIETLISLGVDGIITDYPDLFFEK 271
               SCOP domains d3ch0a_ A: automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3ch0A00 A:0-271 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee...........hhhhhhhhhhhh..eeeeeeee.....eee............ee..ee....hhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhh...eeeeee..hhhhh.....hhhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh...eeeeee....hhhhhhh.......eeee.hhhhhhhhhhhhhhh..ee......hhhhhhhhhhhh..eeee.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ch0 A   0 GmIQVPASFDIQGHRGCRGLLPENTIAAFTKALLLGVTTLEFDLVISKDNRVVVSHDTFFHHEITmmVDGEDVTEANEKNFNLYAmNYADIKEIDVGmKTHPRFKSQKKVPAVKPLFRELIETAEKLSAKIQYNGEIKSTVEGDNIDHPNIALFCDLVVAEIKKAHITDRFTLQSFDVRALEYmHSQYPDIKLSYLVETKGTLKKQLEKLSFTPAVYSPDVTLVSKKDIDAAHKLGmRVIPWTVNTKEEIETLISLGVDGIITDYPDLFFEK 271
                             |       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       259       269  
                             |                                                              65-MSE              85-MSE      97-MSE                                                                               183-MSE                                              236-MSE                               
                             1-MSE                                                           66-MSE

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Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q11WD4_CYTH3 | Q11WD4)

molecular function
	GO:0008889	glycerophosphodiester phosphodiesterase activity	Catalysis of the reaction: a glycerophosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate.
	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.
	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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