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(-) Description

Title :  SM ENDONUCLEASE FROM SERATIA MARCENSCENS AT 1.1 A RESOLUTION
 
Authors :  V. V. Lunin, M. Perbandt, C. H. Betzel, A. M. Mikhailov
Date :  21 Nov 00  (Deposition) - 06 Dec 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Endonuclease, Hydrolase, Nuclease, Magnesium, Signal (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. V. Shlyapnikov, V. V. Lunin, M. Perbandt, K. M. Polyakov, V. Y. Lunin, V. M. Levdikov, C. Betzel, A. M. Mikhailov
Atomic Structure Of The Serratia Marcescens Endonuclease At 1. 1 A Resolution And The Enzyme Reaction Mechanism.
Acta Crystallogr. , Sect. D V. 56 567 2000
PubMed-ID: 10771425  |  Reference-DOI: 10.1107/S090744490000322X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEASE SM2 ISOFORM
    ChainsA, B
    EC Number3.1.30.2
    EngineeredYES
    Expression SystemSERRATIA MARCESCENS
    Expression System Taxid615
    Organism ScientificSERRATIA MARCESCENS
    Organism Taxid615
    Other DetailsMG BINDING SITE AT RESIDUE 127

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2SO44Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:57 , ASN A:119 , HOH A:939 , HOH A:1136 , HOH A:1163 , HOH A:1246 , HOH A:1248BINDING SITE FOR RESIDUE SO4 A 801
2AC2SOFTWAREASN A:20 , ARG B:57 , ARG B:87 , HIS B:89 , ASN B:119 , HOH B:948 , HOH B:1138 , HOH B:1139 , HOH B:1189 , HOH B:1216 , HOH B:1219BINDING SITE FOR RESIDUE SO4 B 802
3AC3SOFTWAREHOH A:914 , HOH A:938 , THR B:77 , GLY B:78 , ARG B:87 , HOH B:861 , HOH B:870 , HOH B:1107BINDING SITE FOR RESIDUE SO4 B 803
4AC4SOFTWAREARG A:25 , LYS A:84 , TYR A:107 , HOH A:905 , HOH A:964 , HOH A:1153 , HOH A:1174 , HOH A:1233BINDING SITE FOR RESIDUE SO4 A 804
5AC5SOFTWAREASN A:119 , HOH A:1163 , HOH A:1164 , HOH A:1246 , HOH A:1247 , HOH A:1248 , HOH A:1249 , HOH A:1250BINDING SITE FOR RESIDUE MG A 810
6AC6SOFTWAREASN B:119 , HOH B:1216 , HOH B:1217 , HOH B:1218 , HOH B:1219 , HOH B:1220BINDING SITE FOR RESIDUE MG B 811

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:9 -A:13
2A:201 -A:243
3B:9 -B:13
4B:201 -B:243

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1G8T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G8T)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUCLEASE_NON_SPECPS01070 DNA/RNA non-specific endonucleases active site.NUCA_SERMA107-115
 
  2A:86-94
B:86-94

(-) Exons   (0, 0)

(no "Exon" information available for 1G8T)

(-) 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:241
 aligned with NUCA_SERMA | P13717 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:241
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265 
           NUCA_SERMA    26 SIDNCAVGCPTGGSSNVSIVRHAYTLNNNSTTKFANWVAYHITKDTPASGKTRNWKTDPALNPADTLAPADYTGANAALKVDRGHQAPLASLAGVSDWESLNYLSNITPQKSDLNQGAWARLEDQERKLIDRADISSVYTVTGPLYERDMGKLPGTQKAHTIPSAYWKVIFINNSPAVNHYAAFLFDQNTPKGADFCQFRVTVDEIEKRTGLIIWAGLPDDVQASLKSKPGVLPELMGCKN 266
               SCOP domains d1g8ta_ A: Sm endonuclease                                                                                                                                                                                                                        SCOP domains
               CATH domains 1g8tA00 A:5-245 Extracellular Endonuclease, subunit A                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................ee....eeee......eeeeeeee...................hhhhh.hhhhhhhhhhhhheeeee..hhhhhh...hhhhhh....eeeeehhhhhhhhhhhhhhhhhhh.......eeeeeeee...................eeeeeeee........eeeeeee.......hhhhh..hhhhhhhhhh.......hhhhhhhhhh...hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------NUCLEASE_------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g8t A   5 SIDNCAVGCPTGGSSNVSIVRHAYTLNNNSTTKFANWVAYHITKDTPASGKTRNWKTDPALNPADTLAPADYTGANAALKVDRGHQAPLASLAGVSDWESLNYLSNITPQKSDLNQGAWARLEDQERKLIDRADISSVYTVTGPLYERDMGKLPGTQKAHTIPSAYWKVIFINNSPAVNHYAAFLFDQNTPKGADFCQFRVTVDEIEKRTGLIIWAGLPDDVQASLKSKPGVLPELMGCKN 245
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244 

Chain B from PDB  Type:PROTEIN  Length:241
 aligned with NUCA_SERMA | P13717 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:241
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265 
           NUCA_SERMA    26 SIDNCAVGCPTGGSSNVSIVRHAYTLNNNSTTKFANWVAYHITKDTPASGKTRNWKTDPALNPADTLAPADYTGANAALKVDRGHQAPLASLAGVSDWESLNYLSNITPQKSDLNQGAWARLEDQERKLIDRADISSVYTVTGPLYERDMGKLPGTQKAHTIPSAYWKVIFINNSPAVNHYAAFLFDQNTPKGADFCQFRVTVDEIEKRTGLIIWAGLPDDVQASLKSKPGVLPELMGCKN 266
               SCOP domains d1g8tb_ B: Sm endonuclease                                                                                                                                                                                                                        SCOP domains
               CATH domains 1g8tB00 B:5-245 Extracellular Endonuclease, subunit A                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................ee....eeee......eeeeeeee...................hhhhh.hhhhhhhhhhhhheeeee..hhhhhh...hhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhh.....eeeeeeee...................eeeeeeee........eeeeeee.......hhhhh..hhhhhhhhhh.......hhhhhhhhhh...hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------NUCLEASE_------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g8t B   5 SIDNCAVGCPTGGSSNVSIVRHAYTLNNNSTTKFANWVAYHITKDTPASGKTRNWKTDPALNPADTLAPADYTGANAALKVDRGHQAPLASLAGVSDWESLNYLSNITPQKSDLNQGAWARLEDQERKLIDRADISSVYTVTGPLYERDMGKLPGTQKAHTIPSAYWKVIFINNSPAVNHYAAFLFDQNTPKGADFCQFRVTVDEIEKRTGLIIWAGLPDDVQASLKSKPGVLPELMGCKN 245
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244 

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G8T)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NUCA_SERMA | P13717)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NUCA_SERMA | P137171qae 1ql0 1smn 4e3y

(-) Related Entries Specified in the PDB File

1smn EXTRACELLULAR ENDONUCLEASE FROM SERRATIA MARCESCENS