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(-) Description

Title :  CRYSTAL STRUCTURE OF INTEIN HOMING ENDONUCLEASE II
 
Authors :  H. Matsumura, H. Takahashi, T. Inoue, H. Hashimoto, M. Nishioka, S. Fuj M. Takagi, T. Imanaka, Y. Kai
Date :  17 Jun 05  (Deposition) - 18 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Matsumura, H. Takahashi, T. Inoue, T. Yamamoto, H. Hashimoto, M. Nishioka, S. Fujiwara, M. Takagi, T. Imanaka, Y. Kai
Crystal Structure Of Intein Homing Endonuclease Ii Encoded In Dna Polymerase Gene From Hyperthermophilic Archaeon Thermococcus Kodakaraensis Strain Kod1
Proteins V. 63 711 2006
PubMed-ID: 16493661  |  Reference-DOI: 10.1002/PROT.20858

(-) Compounds

Molecule 1 - ENDONUCLEASE PI-PKOII
    Chains: A
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET8C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOCOCCUS KODAKARENSIS
    Organism Taxid: 69014
    Strain: KOD1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 21)

Asymmetric/Biological Unit (3, 21)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MSE9Mod. Amino AcidSELENOMETHIONINE
3SO48Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:75 , THR A:93 , SER A:94 , GLY A:95 , HOH A:2085 , HOH A:2203BINDING SITE FOR RESIDUE SO4 A 1001
02AC2SOFTWAREASN A:56 , ARG A:58 , HOH A:2247BINDING SITE FOR RESIDUE SO4 A 1002
03AC3SOFTWARELYS A:161 , PHE A:164 , ARG A:187 , HIS A:191BINDING SITE FOR RESIDUE SO4 A 1003
04AC4SOFTWAREARG A:186 , ARG A:190 , LEU A:200BINDING SITE FOR RESIDUE SO4 A 1004
05AC5SOFTWARETHR A:262 , GLY A:265 , PHE A:266 , PRO A:339 , LYS A:340 , LYS A:341 , HOH A:2159BINDING SITE FOR RESIDUE SO4 A 1005
06AC6SOFTWARELYS A:441 , HIS A:449 , SER A:469 , PRO A:470 , GLN A:471 , HOH A:2193BINDING SITE FOR RESIDUE SO4 A 1006
07AC7SOFTWARELYS A:418 , TYR A:429 , HOH A:2039 , HOH A:2246 , HOH A:2252 , HOH A:2253 , HOH A:2256BINDING SITE FOR RESIDUE SO4 A 1007
08AC8SOFTWAREARG A:83 , ARG A:89 , HOH A:2233BINDING SITE FOR RESIDUE SO4 A 1008
09AC9SOFTWAREILE A:156 , LYS A:161 , PHE A:164 , HIS A:191 , TYR A:220 , GLU A:254 , GLU A:257 , TRP A:258BINDING SITE FOR RESIDUE GOL A 2001
10BC1SOFTWAREVAL A:134 , ASN A:136 , LEU A:140 , ASP A:211 , HOH A:2104 , HOH A:2164 , HOH A:2217BINDING SITE FOR RESIDUE GOL A 2002
11BC2SOFTWAREASN A:136 , LEU A:208 , ASP A:209 , TRP A:210 , ASP A:211 , LEU A:252 , HOH A:2164BINDING SITE FOR RESIDUE GOL A 2003
12BC3SOFTWARETHR A:144 , PRO A:145 , GLU A:146 , HOH A:2079 , HOH A:2208 , HOH A:2209BINDING SITE FOR RESIDUE GOL A 2006

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CW8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CW8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CW8)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTEIN_N_TERPS50817 Intein N-terminal splicing motif profile.DPOL_THEKO407-470
888-951		  1-
A:37-100
2INTEIN_ENDONUCLEASEPS50819 Intein DOD-type homing endonuclease domain profile.DPOL_THEKO524-665
1132-1265		  1-
A:281-414
3INTEIN_C_TERPS50818 Intein C-terminal splicing motif profile.DPOL_THEKO745-767
1365-1389		  1-
A:514-537

(-) Exons   (0, 0)

(no "Exon" information available for 2CW8)

(-) Sequences/Alignments

Asymmetric/Biological 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:537
 aligned with DPOL_THEKO | P77933 from UniProtKB/Swiss-Prot  Length:1671

    Alignment length:537
                                   861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381       
          DPOL_THEKO    852 SILPEEWLPVLEEGEVHFVRIGELIDRMMEENAGKVKREGETEVLEVSGLEVPSFNRRTKKAELKRVKALIRHDYSGKVYTIRLKSGRRIKITSGHSLFSVRNGELVEVTGDELKPGDLVAVPRRLELPERNHVLNLVELLLGTPEEETLDIVMTIPVKGKKNFFKGMLRTLRWIFGEEKRPRTARRYLRHLEDLGYVRLKKIGYEVLDWDSLKNYRRLYEALVENVRYNGNKREYLVEFNSIRDAVGIMPLKELKEWKIGTLNGFRMSPLIEVDESLAKLLGYYVSEGYARKQRNPKNGWSYSVKLYNEDPEVLDDMERLASRFFGKVRRGRNYVEIPKKIGYLLFENMCGVLAENKRIPEFVFTSPKGVRLAFLEGYFIGDGDVHPNKRLRLSTKSELLANQLVLLLNSVGVSAVKLGHDSGVYRVYINEELPFVKLDKKKNAYYSHVIPKEVLSEVFGKVFQKNVSPQTFRKMVEDGRLDPEKAQRLSWLIEGDVVLDRVESVDVEDYDGYVYDLSVEDNENFLVGFGLVYAHN 1388
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee..eeeeeehhhhhhhhhhhhhhhheee..eeeee...eeeeee......eeeeeeeeeeeeeeeeeeeeeee....eeeee...eeeeee..eeeeee........eeeee..........eeehhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhh.......hhhhhhhhhhhhh.eee....eee.hhhhhhhhhhhhhhhhhhhee.....eee.hhhhhhhhhh..hhhhhh..eee.....eee.eee.hhhhhhhhhhhhhheeeeee.......eeeeeee..hhhhhhhhhhhhhhhhh..ee...eeee.hhhhhhhhhhhhh.hhhhh..hhhhh..hhhhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhhh....eeeee....eeeee...............hhhhh.hhhhhhhhhh.......hhhhhhhhhhh...hhhhhh.hhhhhhh.eeeeeeeeeeeeeeeeeeeeeee....eeee....eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------INTEIN_N_TER  PDB: A:37-100 UniProt: 888-951                    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------INTEIN_ENDONUCLEASE  PDB: A:281-414 UniProt: 1132-1265                                                                                ---------------------------------------------------------------------------------------------------INTEIN_C_TER             PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2cw8 A    1 SILPEEWLPVLEEGEVHFVRIGELIDRmmEENAGKVKREGETEVLEVSGLEVPSFNRRTNKAELKRVKALIRHDYSGKVYTIRLKSGRRIKITSGHSLFSVRNGELVEVTGDELKPGDLVAVPRRLELPERNHVLNLVELLLGTPEEETLDIVmTIPVKGKKNFFKGmLRTLRWIFGEEKRPRTARRYLRHLEDLGYVRLKKIGYEVLDWDSLKNYRRLYEALVENVRYNGNKREYLVEFNSIRDAVGImPLKELKEWKIGTLNGFRmRKLIEVDESLAKLLGYYVSEGYARKQRNPKNGWSYSVKLYNEDPEVLDDmERLASRFFGKVRRGRNYVEIPKKIGYLLFENmCGVLAENKRIPEFVFTSPKGVRLAFLEGYFIGDGDVHPNKRLRLSTKSELLANQLVLLLNSVGVSAVKLGHDSGVYRVYINEELPFVKLDKKKNAYYSHVIPKEVLSEVFGKVFQKNVSPQTFRKmVEDGRLDPEKAQRLSWLIEGDVVLDRVESVDVEDYDGYVYDLSVEDNENFLVGFGLVYAHN  537
                                    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       350       360       370       380       390       400       410       420       430       440       450       460       470     | 480       490       500       510       520       530       
                                                      28-MSE                                                                                                                       154-MSE       168-MSE                                                                           250-MSE           268-MSE                                           318-MSE                         350-MSE                                                                                                                       476-MSE                                                         
                                                       29-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 2CW8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2CW8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CW8)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DPOL_THEKO | P77933)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0016539    intein-mediated protein splicing    The removal of an internal amino acid sequence (an intein) from a protein during protein maturation; the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues.
    GO:0006314    intron homing    Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        DPOL_THEKO | P77933: 1wn7 1wns 2cw7 4k8z

(-) Related Entries Specified in the PDB File

2cw7