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(-) Description

Title :  CRYSTAL STRUCTURE OF ENDONUCLEASE/EXONUCLEASE/PHOSPHATASE FAMILY PROTEIN FROM BACTEROIDES THETAIOTAOMICRON, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET BTR318A
 
Authors :  A. Kuzin, M. Su, J. Seetharaman, M. Mao, R. Xiao, C. Ciccosanti, D. Lee, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt Northeast Structural Genomics Consortium (Nesg)
Date :  27 Apr 10  (Deposition) - 26 May 10  (Release) - 26 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kuzin, M. Su, J. Seetharaman, M. Mao, R. Xiao, C. Ciccosanti, D. Lee, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Northeast Structural Genomics Consortium Target Btr318A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE ENDONUCLEASE/EXONUCLEASE/PHOSPHATASE FAMILY PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)+ MAGIC
    Expression System Taxid: 469008
    Expression System Vector: PET 21-23C
    Gene: BT_3783
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 818

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 46)

Asymmetric Unit (5, 46)
No.NameCountTypeFull Name
1ACY6Ligand/IonACETIC ACID
2BR14Ligand/IonBROMIDE ION
3MSE16Mod. Amino AcidSELENOMETHIONINE
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
5UNL8Ligand/IonUNKNOWN LIGAND
Biological Unit 1 (3, 19)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2BR-1Ligand/IonBROMIDE ION
3MSE8Mod. Amino AcidSELENOMETHIONINE
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
5UNL8Ligand/IonUNKNOWN LIGAND
Biological Unit 2 (3, 13)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2BR-1Ligand/IonBROMIDE ION
3MSE8Mod. Amino AcidSELENOMETHIONINE
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
5UNL-1Ligand/IonUNKNOWN LIGAND

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:248 , ARG A:249 , HOH A:610 , LEU B:210 , HOH B:358 , HOH B:683BINDING SITE FOR RESIDUE ACY A 1310
02AC2SOFTWAREASP A:108 , LYS A:161 , HOH A:419 , HOH A:430 , HOH A:1187 , ASP B:75BINDING SITE FOR RESIDUE ACY A 1311
03AC3SOFTWAREARG A:151 , SER A:187BINDING SITE FOR RESIDUE BR A 299
04AC4SOFTWAREHIS A:296 , HOH A:458BINDING SITE FOR RESIDUE BR A 300
05AC5SOFTWARELEU A:54 , HIS A:55BINDING SITE FOR RESIDUE BR A 301
06AC6SOFTWAREASP A:131BINDING SITE FOR RESIDUE BR A 302
07AC7SOFTWAREARG B:249BINDING SITE FOR RESIDUE ACY B 1310
08AC8SOFTWAREGLN B:40 , LEU B:64 , PRO B:65 , GLY B:66BINDING SITE FOR RESIDUE BR B 299
09AC9SOFTWAREARG B:151 , SER B:187BINDING SITE FOR RESIDUE BR B 300
10BC1SOFTWAREHIS B:55BINDING SITE FOR RESIDUE BR B 301
11BC2SOFTWAREARG C:249 , VAL C:251 , HOH C:1014BINDING SITE FOR RESIDUE ACY C 1310
12BC3SOFTWARELYS C:148 , ARG C:151 , SER C:187BINDING SITE FOR RESIDUE BR C 299
13BC4SOFTWAREARG C:74 , ILE C:121BINDING SITE FOR RESIDUE BR C 300
14BC5SOFTWAREASP C:199 , LYS C:203 , HOH C:390 , HOH C:434BINDING SITE FOR RESIDUE BR C 301
15BC6SOFTWAREPRO A:234 , SER A:235 , HIS A:237 , ASP A:290 , HIS A:294 , HIS A:296 , ASP C:205 , HIS C:237 , LYS C:239 , HOH C:334 , HOH C:374BINDING SITE FOR RESIDUE PEG C 306
16BC7SOFTWAREARG D:249BINDING SITE FOR RESIDUE ACY D 1310
17BC8SOFTWAREASP A:205 , HIS A:237 , LYS A:239 , SER C:235 , HIS C:237 , PHE C:289 , ASP C:290 , HIS C:293 , HIS C:294 , HIS C:296 , HOH C:725BINDING SITE FOR RESIDUE PEG C 307
18BC9SOFTWAREPHE D:214 , THR D:223 , HOH D:323BINDING SITE FOR RESIDUE ACY D 1311
19CC1SOFTWAREGLN D:40 , PRO D:65 , GLY D:66 , HOH D:685BINDING SITE FOR RESIDUE BR D 299
20CC2SOFTWAREHIS D:55BINDING SITE FOR RESIDUE BR D 300
21CC3SOFTWARELYS D:148 , SER D:187BINDING SITE FOR RESIDUE BR D 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MPR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MPR)

(-) 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:282
 aligned with Q8A183_BACTN | Q8A183 from UniProtKB/TrEMBL  Length:315

    Alignment length:298
                                                                                                                                                                                                                                                                                                                                315   
                                    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    |   
         Q8A183_BACTN    21 SYQPTSLTVASYNLRNANGSDSARGDGWGQRYPVIAQMVQYHDFDIFGTQECFLHQLKDMKEALPGYDYIGVGRDDGKDKGEHSAIFYRTDKFDIVEKGDFWLSETPDVPSKGWDAVLPRICSWGHFKCKDTGFEFLFFNLHMDHIGKKARVESAFLVQEKMKELGRGKNLPAILTGDFNVDQTHQSYDAFVSKGVLCDSYEKCDYRYALNGTFNNFDPNSFTESRIDHIFVSPSFHVKRYGVLTDTYRSVRENSKKEDVRDCPEEITIKAYEARTPSDHFPVKVELVFDQRQQK---   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee....hhhhhhhh.hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh..eeee...............eeee...eeeeeeeeee..................eeeeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhh.......eeeeee......hhhhhhhhh....eehhhhh.eee...................eeeee....eeeeeee....eeee..----------------..eeee.......eeeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mpr A   1 SYQPTSLTVASYNLRNANGSDSARGDGWGQRYPVIAQmVQYHDFDIFGTQECFLHQLKDmKEALPGYDYIGVGRDDGKDKGEHSAIFYRTDKFDIVEKGDFWLSETPDVPSKGWDAVLPRICSWGHFKCKDTGFEFLFFNLHmDHIGKKARVESAFLVQEKmKELGRGKNLPAILTGDFNVDQTHQSYDAFVSKGVLCDSYEKCDYRYALNGTFNNFDPNSFTESRIDHIFVSPSFHVKRYGVLTDTYRSVRE----------------KAYEARTPSDHFPVKVELVFDLEHHHHHH 298
                                    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  |      -       270       280       290        
                                                                38-MSE                60-MSE                                                                            143-MSE            162-MSE                                                                                    253              270                            


Chain B from PDB  Type:PROTEIN  Length:271
 aligned with Q8A183_BACTN | Q8A183 from UniProtKB/TrEMBL  Length:315

    Alignment length:290
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311
         Q8A183_BACTN    22 YQPTSLTVASYNLRNANGSDSARGDGWGQRYPVIAQMVQYHDFDIFGTQECFLHQLKDMKEALPGYDYIGVGRDDGKDKGEHSAIFYRTDKFDIVEKGDFWLSETPDVPSKGWDAVLPRICSWGHFKCKDTGFEFLFFNLHMDHIGKKARVESAFLVQEKMKELGRGKNLPAILTGDFNVDQTHQSYDAFVSKGVLCDSYEKCDYRYALNGTFNNFDPNSFTESRIDHIFVSPSFHVKRYGVLTDTYRSVRENSKKEDVRDCPEEITIKAYEARTPSDHFPVKVELVFDQ 311
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....hhhhhhhh.hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh..eeee...............eeee...eeeeeeeeee..................eeeeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhhhh---..eeeeee......hhhhhhhhh....eehhhhh.eee...................eeeee....eeeeeee....eeee..----------------..eeee.......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mpr B   2 YQPTSLTVASYNLRNANGSDSARGDGWGQRYPVIAQmVQYHDFDIFGTQECFLHQLKDmKEALPGYDYIGVGRDDGKDKGEHSAIFYRTDKFDIVEKGDFWLSETPDVPSKGWDAVLPRICSWGHFKCKDTGFEFLFFNLHmDHIGKKARVESAFLVQEKmKELGR---LPAILTGDFNVDQTHQSYDAFVSKGVLCDSYEKCDYRYALNGTFNNFDPNSFTESRIDHIFVSPSFHVKRYGVLTDTYRSVRE----------------KAYEARTPSDHFPVKVELVFDL 291
                                    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 |       -       271       281       291
                                                               38-MSE                60-MSE                                                                            143-MSE            162-MSE7 171                                                                               253              270                     


Chain C from PDB  Type:PROTEIN  Length:281
 aligned with Q8A183_BACTN | Q8A183 from UniProtKB/TrEMBL  Length:315

    Alignment length:298
                                                                                                                                                                                                                                                                                                                                315   
                                    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    |   
         Q8A183_BACTN    21 SYQPTSLTVASYNLRNANGSDSARGDGWGQRYPVIAQMVQYHDFDIFGTQECFLHQLKDMKEALPGYDYIGVGRDDGKDKGEHSAIFYRTDKFDIVEKGDFWLSETPDVPSKGWDAVLPRICSWGHFKCKDTGFEFLFFNLHMDHIGKKARVESAFLVQEKMKELGRGKNLPAILTGDFNVDQTHQSYDAFVSKGVLCDSYEKCDYRYALNGTFNNFDPNSFTESRIDHIFVSPSFHVKRYGVLTDTYRSVRENSKKEDVRDCPEEITIKAYEARTPSDHFPVKVELVFDQRQQK---   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee....hhhhhhh..hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh..eeee...............eeee...eeeeeeeeee..................eeeeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhh.......eeeeee......hhhhhhhhh....eehhhhh.eee...................eeeee....eeeeeee....eeee.-----------------..eeee.......eeeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mpr C   1 SYQPTSLTVASYNLRNANGSDSARGDGWGQRYPVIAQmVQYHDFDIFGTQECFLHQLKDmKEALPGYDYIGVGRDDGKDKGEHSAIFYRTDKFDIVEKGDFWLSETPDVPSKGWDAVLPRICSWGHFKCKDTGFEFLFFNLHmDHIGKKARVESAFLVQEKmKELGRGKNLPAILTGDFNVDQTHQSYDAFVSKGVLCDSYEKCDYRYALNGTFNNFDPNSFTESRIDHIFVSPSFHVKRYGVLTDTYRSVR-----------------KAYEARTPSDHFPVKVELVFDLEHHHHHH 298
                                    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 |       -       270       280       290        
                                                                38-MSE                60-MSE                                                                            143-MSE            162-MSE                                                                                   252               270                            


Chain D from PDB  Type:PROTEIN  Length:275
 aligned with Q8A183_BACTN | Q8A183 from UniProtKB/TrEMBL  Length:315

    Alignment length:290
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312
         Q8A183_BACTN    23 QPTSLTVASYNLRNANGSDSARGDGWGQRYPVIAQMVQYHDFDIFGTQECFLHQLKDMKEALPGYDYIGVGRDDGKDKGEHSAIFYRTDKFDIVEKGDFWLSETPDVPSKGWDAVLPRICSWGHFKCKDTGFEFLFFNLHMDHIGKKARVESAFLVQEKMKELGRGKNLPAILTGDFNVDQTHQSYDAFVSKGVLCDSYEKCDYRYALNGTFNNFDPNSFTESRIDHIFVSPSFHVKRYGVLTDTYRSVRENSKKEDVRDCPEEITIKAYEARTPSDHFPVKVELVFDQR 312
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------Exo_endo_phos-3mprD01 D:10-280                                                                                                                                                                                                                                                 ------------ Pfam domains (1)
           Pfam domains (2) -------Exo_endo_phos-3mprD02 D:10-280                                                                                                                                                                                                                                                 ------------ Pfam domains (2)
           Pfam domains (3) -------Exo_endo_phos-3mprD03 D:10-280                                                                                                                                                                                                                                                 ------------ Pfam domains (3)
           Pfam domains (4) -------Exo_endo_phos-3mprD04 D:10-280                                                                                                                                                                                                                                                 ------------ Pfam domains (4)
         Sec.struct. author ..eeeeeeeee....hhhhhhh..hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh..eeee...............eeee...eeeeeeeeee..................eeeeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhhh......eeeeee......hhhhhhhhh....eehhhhh.eee...................eeeee....eeeeeee....eeeee..---------------.eeeee.......eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mpr D   3 QPTSLTVASYNLRNANGSDSARGDGWGQRYPVIAQmVQYHDFDIFGTQECFLHQLKDmKEALPGYDYIGVGRDDGKDKGEHSAIFYRTDKFDIVEKGDFWLSETPDVPSKGWDAVLPRICSWGHFKCKDTGFEFLFFNLHmDHIGKKARVESAFLVQEKmKELGRGKNLPAILTGDFNVDQTHQSYDAFVSKGVLCDSYEKCDYRYALNGTFNNFDPNSFTESRIDHIFVSPSFHVKRYGVLTDTYRSVREN---------------KAYEARTPSDHFPVKVELVFDLE 292
                                    12        22        32     |  42        52       |62        72        82        92       102       112       122       132       142|      152       162       172       182       192       202       212       222       232       242       252 |       -       272       282       292
                                                              38-MSE                60-MSE                                                                            143-MSE            162-MSE                                                                                     254             270
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 3MPR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: Exo_endo_phos] (21)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8A183_BACTN | Q8A183)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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  3mpr
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  Q8A183_BACTN | Q8A183
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 Related Entries

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

UniProtKB/TrEMBL
        Q8A183_BACTN | Q8A183: 4c1r

(-) Related Entries Specified in the PDB File

3g6s 39% IDENTITY RELATED ID: BTR318A RELATED DB: TARGETDB