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(-) Description

Title :  P1 NUCLEASE IN COMPLEX WITH A SUBSTRATE ANALOG
 
Authors :  C. Romier, D. Suck
Date :  28 May 97  (Deposition) - 03 Dec 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Endonuclease, P1 Nuclease, Reaction Mechanism, Thiophosphorylated Oligonucleotides, Glycosylated Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Romier, R. Dominguez, A. Lahm, O. Dahl, D. Suck
Recognition Of Single-Stranded Dna By Nuclease P1: High Resolution Crystal Structures Of Complexes With Substrate Analogs.
Proteins V. 32 414 1998 (for further references see the PDB file header)

(-) Compounds

Molecule 1 - P1 NUCLEASE
    Chains: A
    EC Number: 3.1.30.1
    Organism Scientific: PENICILLIUM CITRINUM
    Organism Taxid: 5077

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1ADS1Ligand/IonADENOSINE-5'-(DITHIO)PHOSPHATE
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
3THS3Ligand/IonTHYMIDINE-5'-(DITHIO)PHOSPHATE
4ZN4Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:92 , TYR A:93 , ARG A:96 , GLU A:109 , NAG A:282 , HOH A:551BINDING SITE FOR RESIDUE NAG A 281
02AC2SOFTWARETRP A:55 , NAG A:281 , HOH A:516BINDING SITE FOR RESIDUE NAG A 282
03AC3SOFTWAREASN A:197 , SER A:199 , HOH A:540BINDING SITE FOR RESIDUE NAG A 285
04AC4SOFTWAREASN A:138 , HOH A:552BINDING SITE FOR RESIDUE NAG A 287
05AC5SOFTWAREASP A:45 , HIS A:60 , HIS A:116 , ASP A:120 , ZN A:273BINDING SITE FOR RESIDUE ZN A 271
06AC6SOFTWAREHIS A:126 , HIS A:149 , ASP A:153 , THS A:295BINDING SITE FOR RESIDUE ZN A 272
07AC7SOFTWARETRP A:1 , HIS A:6 , ASP A:120 , ZN A:271BINDING SITE FOR RESIDUE ZN A 273
08AC8SOFTWAREHIS A:15 , GLU A:181 , HIS A:223 , HOH A:539BINDING SITE FOR RESIDUE ZN A 274
09AC9SOFTWAREASN A:71 , ASN A:73 , PHE A:141 , TYR A:144 , ASP A:146 , TYR A:155 , THS A:293 , HOH A:441BINDING SITE FOR RESIDUE ADS A 292
10BC1SOFTWAREASP A:66 , ASN A:67 , ASN A:73 , ASP A:75 , ARG A:78 , HIS A:164 , ADS A:292 , THS A:294 , HOH A:519BINDING SITE FOR RESIDUE THS A 293
11BC2SOFTWAREGLU A:77 , LYS A:136 , THS A:293 , THS A:295BINDING SITE FOR RESIDUE THS A 294
12BC3SOFTWAREPHE A:61 , ASP A:63 , LEU A:125 , HIS A:126 , ASN A:135 , HIS A:149 , ASP A:153 , ZN A:272 , THS A:294 , HOH A:428 , HOH A:429BINDING SITE FOR RESIDUE THS A 295

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:72 -A:217
2A:80 -A:85

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:68 -Pro A:69
2Tyr A:234 -Pro A:235

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1AK0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1AK0)

(-) Exons   (0, 0)

(no "Exon" information available for 1AK0)

(-) 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:264
 aligned with NUP1_PENCI | P24289 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:264
                                    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    
           NUP1_PENCI     1 WGALGHATVAYVAQHYVSPEAASWAQGILGSSSSSYLASIASWADEYRLTSAGKWSASLHFIDAEDNPPTNCNVDYERDCGSSGCSISAIANYTQRVSDSSLSSENHAEALRFLVHFIGDMTQPLHDEAYAVGGNKINVTFDGYHDNLHSDWDTYMPQKLIGGHALSDAESWAKTLVQNIESGNYTAQAIGWIKGDNISEPITTATRWASDANALVCTVVMPHGAAALQTGDLYPTYYDSVIDTIELQIAKGGYRLANWINEIH 264
               SCOP domains d1ak0a_ A: P1 nuclease                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1ak0A00 A:1-264 P1 Nuclease                                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh..hhhhhhhhhhh........hhh..hhhhhhh....hhhhhhh...............hhhh......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.hhhh..hhhh....eeee..eeeehhhhhh.hhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.......hhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ak0 A   1 WGALGHATVAYVAQHYVSPEAASWAQGILGSSSSSYLASIASWADEYRLTSAGKWSASLHFIDAEDNPPTNCNVDYERDCGSSGCSISAIANYTQRVSDSSLSSENHAEALRFLVHFIGDMTQPLHDEAYAVGGNKINVTFDGYHDNLHSDWDTYMPQKLIGGHALSDAESWAKTLVQNIESGNYTAQAIGWIKGDNISEPITTATRWASDANALVCTVVMPHGAAALQTGDLYPTYYDSVIDTIELQIAKGGYRLANWINEIH 264
                                    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
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AK0)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NUP1_PENCI | P24289)
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:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    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:0006308    DNA catabolic process    The cellular DNA metabolic process resulting in the breakdown 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: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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