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(-) Description

Title :  CRYSTAL STRUCTURE OF CYTOSOLIC NUCLEOTIDASE II (LPG0095) IN COMPLEX WITH GMP FROM LEGIONELLA PNEUMOPHILA, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET LGR1
 
Authors :  B. Srinivisan, F. Forouhar, A. Shukla, C. Sampangi, S. Kulkarni, M. Aba J. Seetharaman, S. Lew, L. Mao, T. B. Acton, R. Xiao, J. K. Everett, G. M. Montelione, L. Tong, H. Balaram, Northeast Structural Genomi Consortium (Nesg)
Date :  17 Jan 14  (Deposition) - 26 Feb 14  (Release) - 09 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.53
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Keywords :  Structural Genomics, Psi-Biology, Northeast Structural Genomics Consortium, Nesg, 3-Domained Structure That Resembles Had, Nucleotidase. It Catalyzes The Breakdown Of Selected Nucleoside Monophosphates, Cytosol, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Srinivasan, F. Forouhar, A. Shukla, C. Sampangi, S. Kulkarni, M. Abashidze, J. Seetharaman, S. Lew, L. Mao, T. B. Acton, R. Xiao, J. K. Everett, G. T. Montelione, L. Tong, H. Balaram
Allosteric Regulation And Substrate Activation In Cytosolic Nucleotidase Ii From Legionella Pneumophila.
Febs J. V. 281 1613 2014
PubMed-ID: 24456211  |  Reference-DOI: 10.1111/FEBS.12727

(-) Compounds

Molecule 1 - CYTOSOLIC IMP-GMP SPECIFIC 5'-NUCLEOTIDASE
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21
    Expression System StrainBL21(DE3)+MAGIC
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneLPG0095
    Organism ScientificLEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA
    Organism Taxid272624
    StrainPHILADELPHIA 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (2x)AB  
Biological Unit 2 (1x)AB  
Biological Unit 3 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
15GP2Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2MG3Ligand/IonMAGNESIUM ION
3PO48Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
15GP2Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PO48Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
15GP1Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PO44Ligand/IonPHOSPHATE ION
Biological Unit 3 (2, 5)
No.NameCountTypeFull Name
15GP1Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:86 , TYR A:87 , ASP A:308 , TYR A:421 , ARG A:425 , ARG B:86 , TYR B:87 , TYR B:421BINDING SITE FOR RESIDUE 5GP A 501
02AC2SOFTWAREASP A:23 , MET A:24 , ASP A:25 , THR A:209 , ASN A:210 , LYS A:247 , HOH A:655BINDING SITE FOR RESIDUE PO4 A 502
03AC3SOFTWAREARG A:10 , LYS A:313 , TRP A:318 , ARG A:319 , THR A:320 , PHE A:426 , CYS A:428BINDING SITE FOR RESIDUE PO4 A 503
04AC4SOFTWAREASP B:23 , MET B:24 , ASP B:25 , THR B:209 , ASN B:210 , SER B:211 , LYS B:247 , MG B:503 , HOH B:667BINDING SITE FOR RESIDUE PO4 B 501
05AC5SOFTWARETYR A:113 , ARG B:10 , LYS B:313 , ARG B:319 , THR B:320 , PHE B:426 , CYS B:428BINDING SITE FOR RESIDUE PO4 B 502
06AC6SOFTWAREASP B:23 , ASP B:25 , ASP B:303 , PO4 B:501 , HOH B:667BINDING SITE FOR RESIDUE MG B 503
07AC7SOFTWAREARG C:86 , TYR C:87 , ASP C:308 , TYR C:421 , ARG D:86 , TYR D:87 , TYR D:421BINDING SITE FOR RESIDUE 5GP C 501
08AC8SOFTWAREASP C:23 , MET C:24 , ASP C:25 , THR C:209 , ASN C:210 , SER C:211 , LYS C:247 , MG C:504 , HOH C:648BINDING SITE FOR RESIDUE PO4 C 502
09AC9SOFTWAREARG C:10 , LYS C:313 , TRP C:318 , ARG C:319 , THR C:320 , PHE C:426 , CYS C:428BINDING SITE FOR RESIDUE PO4 C 503
10BC1SOFTWAREASP C:23 , ASP C:25 , ASP C:303 , PO4 C:502 , HOH C:648BINDING SITE FOR RESIDUE MG C 504
11BC2SOFTWAREASP D:23 , MET D:24 , ASP D:25 , THR D:209 , ASN D:210 , SER D:211 , LYS D:247 , MG D:503 , HOH D:636BINDING SITE FOR RESIDUE PO4 D 501
12BC3SOFTWARETYR C:113 , ARG D:10 , LYS D:313 , ARG D:319 , THR D:320 , PHE D:426 , CYS D:428BINDING SITE FOR RESIDUE PO4 D 502
13BC4SOFTWAREASP D:23 , ASP D:25 , ASP D:303 , PO4 D:501 , HOH D:636BINDING SITE FOR RESIDUE MG D 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OHF)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:247 -Pro A:248
2Lys B:247 -Pro B:248
3Lys C:247 -Pro C:248
4Lys D:247 -Pro D:248

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OHF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OHF)

(-) Exons   (0, 0)

(no "Exon" information available for 4OHF)

(-) 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:455
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4ohfa_ A: Cytosolic IMP-GMP specific 5'-nucleotidase                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...ee.....eeee.......eehhhhhhhhhhhhhhhhhhhhh..hhhhhhh..hhhhh....eee....eeeee.....eeeeee..ee.hhhhhhhhh...........ee.....hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh....hhhhhh.eeee....hhhhhh...eeee......eee.......eeeee.hhhhhhhhh..hhh.eeeee.....hhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh........ee..eehhhhhhhhhhh.eee.hhhhhhh.....ee...hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ohf A   5 KVFVNRIINMRKIKLIGLDMDHTLIRYNSKNFESLVYDLVKERLAESFHYPEEIKKFKFNFDDAIRGLVIDSKNGNILKLSRYGAIRLSYHGTKQISFSDQKKIYRSIYVDLGDPNYMAIDTSFSIAFCILYGQLVDLKDTNPDKMPSYQAIAQDVQYCVDKVHSDGTLKNIIIKNLKKYVIREKEVVEGLKHFIRYGKKIFILTNSEYSYSKLLLDYALSPFLDKGEHWQGLFEFVITLANKPRFFYDNLRFLSVNPENGTMTNVHGPIVPGVYQGGNAKKFTEDLGVGGDEILYIGDHIYGDILRLKKDCNWRTALVVEELGEEIASQIRALPIEKKIGEAMAIKKELEQKYVDLCTRSIDESYDQEIHDLQLQISTVDLQISRLLQEQNSFYNPKWERVFRAGAEESYFAYQVDRFACIYMEKLSDLLEHSPMTYFRANRRLLAHDIDILEH 462
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364    || 377       387       397       407       417       427       437       447       457     
                                                                                                                                                                                                                                                                                                                                                                                                      369|                                                                                         
                                                                                                                                                                                                                                                                                                                                                                                                       373                                                                                         

Chain B from PDB  Type:PROTEIN  Length:458
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4ohfb_ B: Cytosolic IMP-GMP specific 5'-nucleotidase                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee...ee.hhh.eeee.......eehhhhhhhhhhhhhhhhhhhhh..hhhhhhh..hhhhh....eee....eeeee.....eeeeee..ee.hhhhhhhhhh..........ee.....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh....hhhhhh.eeee....hhhhhh...eeee......eee.......eeeee.hhhhhhhhh..hhh.eeeee.....hhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........ee..eehhhhhhhhhhh.eee.hhhhhhh.....ee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ohf B   2 DTHKVFVNRIINMRKIKLIGLDMDHTLIRYNSKNFESLVYDLVKERLAESFHYPEEIKKFKFNFDDAIRGLVIDSKNGNILKLSRYGAIRLSYHGTKQISFSDQKKIYRSIYVDLGDPNYMAIDTSFSIAFCILYGQLVDLKDTNPDKMPSYQAIAQDVQYCVDKVHSDGTLKNIIIKNLKKYVIREKEVVEGLKHFIRYGKKIFILTNSEYSYSKLLLDYALSPFLDKGEHWQGLFEFVITLANKPRFFYDNLRFLSVNPENGTMTNVHGPIVPGVYQGGNAKKFTEDLGVGGDEILYIGDHIYGDILRLKKDCNWRTALVVEELGEEIASQIRALPIEKKIGEAMAIKKELEQKYVDLCTRSIDESSQQYDQEIHDLQLQISTVDLQISRLLQEQNSFYNPKWERVFRAGAEESYFAYQVDRFACIYMEKLSDLLEHSPMTYFRANRRLLAHDIDI 459
                                    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       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451        

Chain C from PDB  Type:PROTEIN  Length:438
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4ohfc_ C: Cytosolic IMP-GMP specific 5'-nucleotidase                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee...ee.....eeee.......eehhhhhhhhhhhhhhhhhhhhh..hhhhhhh..hhhhh....eee....eeeee.....eeeeee..ee.hhhhhhhhh...........ee.....hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh....hhhhhh.eeee....hhhhhh...eeee......eee.......eeeee.hhhhhhhhh..hhh.eeeee.....hhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh........ee..eehhhhhhhhhhh.eee.hhhhhhh.....ee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ohf C   5 KVFVNRIINMRKIKLIGLDMDHTLIRYNSKNFESLVYDLVKERLAESFHYPEEIKKFKFNFDDAIRGLVIDSKNGNILKLSRYGAIRLSYHGTKQISFSDQKKIYRSIYVDLGDPNYMAIDTSFSIAFCILYGQLVDLKDTNPDKMPSYQAIAQDVQYCVDKVHSDGTLKNIIIKNLKKYVIREKEVVEGLKHFIRYGKKIFILTNSEYSYSKLLLDYALSPFLDKGEHWQGLFEFVITLANKPRFFYDNLRFLSVNPENGTMTNVHGPIVPGVYQGGNAKKFTEDLGVGGDEILYIGDHIYGDILRLKKDCNWRTALVVEELGEEIASQIRALPIEKKIGEAMAIKKELEQKYVDLHDLQLQISTVDLQISRLLQEQNSFYNPKWERVFRAGAEESYFAYQVDRFACIYMEKLSDLLEHSPMTYFRANRRLLAHDID 458
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354      |380       390       400       410       420       430       440       450        
                                                                                                                                                                                                                                                                                                                                                                                              361|                                                                                
                                                                                                                                                                                                                                                                                                                                                                                               378                                                                                

Chain D from PDB  Type:PROTEIN  Length:456
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4ohfd_ D: Cytosolic IMP-GMP specific 5'-nucleotidase                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee...ee.hhh.eeee.......eehhhhhhhhhhhhhhhhhhhhh..hhhhhhh..hhhhh....eee....eeeee.....eeeeee..ee.hhhhhhhhhh..........ee.....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh....hhhhhh.eeee....hhhhhh...eeee......eee.......eeeee.hhhhhhhhh..hhh.eeeee.....hhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ee..eehhhhhhhhhhh.eee.hhhhhhh.....ee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ohf D   3 THKVFVNRIINMRKIKLIGLDMDHTLIRYNSKNFESLVYDLVKERLAESFHYPEEIKKFKFNFDDAIRGLVIDSKNGNILKLSRYGAIRLSYHGTKQISFSDQKKIYRSIYVDLGDPNYMAIDTSFSIAFCILYGQLVDLKDTNPDKMPSYQAIAQDVQYCVDKVHSDGTLKNIIIKNLKKYVIREKEVVEGLKHFIRYGKKIFILTNSEYSYSKLLLDYALSPFLDKGEHWQGLFEFVITLANKPRFFYDNLRFLSVNPENGTMTNVHGPIVPGVYQGGNAKKFTEDLGVGGDEILYIGDHIYGDILRLKKDCNWRTALVVEELGEEIASQIRALPIEKKIGEAMAIKKELEQKYVDLCTRSIDESSQQYDQEIHDLQLQISTVDLQISRLLQEQNSFYNPKWERVFRAGAEESYFAYQVDRFACIYMEKLSDLLEHSPMTYFRANRRLLAHDID 458
                                    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       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452      

   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OHF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OHF)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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        Q5ZZB6_LEGPH | Q5ZZB62bde 4g63

(-) Related Entries Specified in the PDB File

4g63 CRYSTAL STRUCTURE OF CYTOSOLIC IMP-GMP SPECIFIC 5'- NUCLEOTIDASE (LPG0095) IN COMPLEX WITH PHOSPHATE IONS FROM LEGIONELLA PNEUMOPHILA,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET LGR1 RELATED ID: NESG-LGR1 RELATED DB: TARGETTRACK