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(-) Description

Title :  LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH MG GMPPNP
 
Authors :  M. Zebisch, P. Schaefer, P. Lauble, N. Straeter
Date :  04 Jun 13  (Deposition) - 17 Jul 13  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Apyrase, Atpase, Adpase, Cd39, Purinergic Signalling, Domain Rotation, Transition State, Ntpdase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Zebisch, M. Krauss, P. Schaefer, P. Lauble, N. Straeter
Crystallographic Snapshots Along The Reaction Pathway Of Nucleoside Triphosphate Diphosphohydrolases
Structure V. 21 1460 2013
PubMed-ID: 23830739  |  Reference-DOI: 10.1016/J.STR.2013.05.016

(-) Compounds

Molecule 1 - ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
    Chains: A, B
    EC Number: 3.6.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 35-393
    Organism Scientific: LEGIONELLA PNEUMOPHILA
    Organism Taxid: 446
    Synonym: NTPDASE1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4MG2Ligand/IonMAGNESIUM ION
5NA1Ligand/IonSODIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:51 , SER A:52 , THR A:53 , ARG A:56 , THR A:118 , ALA A:119 , GLU A:159 , MET A:187 , GLY A:189 , ALA A:190 , SER A:191 , GLN A:231 , THR A:232 , GLY A:298 , GLY A:299 , ASN A:302 , TYR A:346 , LEU A:353 , MG A:1394 , HOH A:2011 , HOH A:2012 , HOH A:2027 , HOH A:2092 , HOH A:2156 , HOH A:2157 , HOH A:2168 , HOH A:2199 , HOH A:2288 , HOH A:2289 , HOH A:2326 , HOH A:2330BINDING SITE FOR RESIDUE GNP A1393
2AC2SOFTWAREGNP A:1393 , HOH A:2011 , HOH A:2012 , HOH A:2156 , HOH A:2168BINDING SITE FOR RESIDUE MG A1394
3AC3SOFTWAREHIS A:224 , PHE A:226 , VAL A:275 , HIS A:276 , GLN A:281 , HOH A:2196 , HOH A:2197 , HOH A:2259 , HOH A:2349 , GLU B:267BINDING SITE FOR RESIDUE MES A1395
4AC4SOFTWAREARG A:122 , HOH A:2098 , ASN B:240 , PRO B:252 , ASP B:253BINDING SITE FOR RESIDUE CL B1396
5AC5SOFTWAREGLU A:233 , HIS A:236 , HOH A:2202 , GLU B:233 , HIS B:236BINDING SITE FOR RESIDUE NA A1396
6AC6SOFTWAREGLY B:51 , SER B:52 , THR B:53 , ARG B:56 , THR B:118 , ALA B:119 , GLU B:159 , MET B:187 , GLY B:189 , ALA B:190 , SER B:191 , GLN B:231 , THR B:232 , GLY B:298 , GLY B:299 , ASN B:302 , TYR B:346 , TYR B:350 , MG B:1398 , HOH B:2010 , HOH B:2011 , HOH B:2024 , HOH B:2103 , HOH B:2155 , HOH B:2156 , HOH B:2166 , HOH B:2294 , HOH B:2310 , HOH B:2311BINDING SITE FOR RESIDUE GNP B1397
7AC7SOFTWAREGNP B:1397 , HOH B:2010 , HOH B:2011 , HOH B:2156 , HOH B:2166BINDING SITE FOR RESIDUE MG B1398
8AC8SOFTWAREASN A:240 , GLU A:267 , HOH A:2213 , HOH A:2215 , HIS B:224 , PHE B:226 , VAL B:275 , HIS B:276 , GLN B:281 , HOH B:2191 , HOH B:2312BINDING SITE FOR RESIDUE MES B1399
9AC9SOFTWAREASN A:240 , ASP A:253 , ARG B:122 , GLY B:156 , HOH B:2108BINDING SITE FOR RESIDUE CL A1397

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:39 -A:44
2A:244 -A:264
3A:330 -A:351
4B:39 -B:44
5B:244 -B:264
6B:330 -B:351

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:82 -Pro A:83
2Lys B:82 -Pro B:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4BRG)

(-) 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:359
 aligned with Q5ZUA2_LEGPH | Q5ZUA2 from UniProtKB/TrEMBL  Length:393

    Alignment length:359
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383         
         Q5ZUA2_LEGPH    34 ADTNPCEKHSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELEYWFRQQSQWQLAEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHR 392
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.eeeeeeee....eeeeeeeeee.....eeeeeeeeeeee..hhhhh..hhhhhhhhhhhhhh.......eeeeeehhhhhh.hhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhhhh.........eeeeee...eeeeeee.......hhh.eeeeee..eeeeeeeeeee..hhhhhhh....hhhhh..............hhhhhhhhhhhhhhh..hhhhhhhhhhhhh...eeeeeehhhhhhh.........eehhhhhhhhhhhhh...hhhhhhhhh....hhhhhhhhhhhhhhhhh..........eee.hhhhh...hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4brg A  34 MDTNPCEKHSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELDYWFRQQSQWQLVEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHR 392
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383         


Chain B from PDB  Type:PROTEIN  Length:361
 aligned with Q5ZUA2_LEGPH | Q5ZUA2 from UniProtKB/TrEMBL  Length:393

    Alignment length:361
                                                                                                                                                                                                                                                                                                                                                                                                393  
                                    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       374       384        |- 
         Q5ZUA2_LEGPH    35 DTNPCEKHSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELEYWFRQQSQWQLAEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHRA--   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.eeeeeeee....eeeeeeeeee.....eeeeeeeeeeee..hhhhh..hhhhhhhhhhhhhh......eeeeeeehhhhhh.hhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhhhhh.........eeeeee...eeeeeee.......hhh.eeeeee..eeeeeeeeeee..hhhhhhh....hhhhh..............hhhhhhhhhhhhhhh..hhhhhhhhhhhhh...eeeeeehhhhhhh.........eeehhhhhhhhhhhh...hhhhhhhhh....hhhhhhhhhhhhhhhhh.........eeee.hhhhh..hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4brg B  35 DTNPCEKHSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELDYWFRQQSQWQLVEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHRALE 395
                                    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       374       384       394
   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 4BRG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5ZUA2_LEGPH | Q5ZUA2)
molecular function
    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: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.

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  3.6.1.5
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 Related Entries

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

UniProtKB/TrEMBL
        Q5ZUA2_LEGPH | Q5ZUA2: 3aap 3aaq 3aar 4br4 4br7 4br9 4bra 4brc 4brd 4bre 4brf 4brh 4bri 4brk 4brl 4brm 4brn 4bro 4brp 4brq 4bvo 4bvp

(-) Related Entries Specified in the PDB File

3cj1 STRUCTURE OF RATTUS NORVEGICUS NTPDASE2
3cj7 STRUCTURE OF RATTUS NORVEGICUS NTPDASE2 IN COMPLEX WITH AMP
3cj9 STRUCTURE OF RATTUS NORVEGICUS NTPDASE2 IN COMPLEX WITH CALCIUM, AMP AND PHOSPHATE
3cja STRUCTURE OF RATTUS NORVEGICUS NTPDASE2 IN COMPLEX WITH CALCIUM AND AMPPNP
4bqz RAT NTPDASE2 IN COMPLEX WITH MG GMPPNP
4br0 RAT NTPDASE2 IN COMPLEX WITH CAAMPNP
4br2 RAT NTPDASE2 IN COMPLEX WITH CA UMPPNP
4br4 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM I, OPEN, APO
4br5 RNNTPDASE2 IN COMPLEX WITH ZNAMPPNP
4br7 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM I, OPEN, APO
4br9 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, APO
4bra LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, MG AMPPNP COMPLEX
4brc LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, MG AMPNP COMPLEX
4brd LEGIONELLA PNEUMOPHILA NTPDASE1 Q193E CRYSTAL FORM II, CLOSED, MG AMPPNP COMPLEX
4bre LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH TRANSITION STATE MIMIC ADENOSINE 5' PHOSPHOVANADATE
4brf LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH A DISTORTED ORTHOMOLYBDATE ION AND AMP
4brh LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH MG AND THIAMINE PHOSPHOVANADATE
4bri LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH MG UMPPNP
4brk LEGIONELLA PNEUMOPHILA NTPDASE1 N302Y VARIANT CRYSTAL FORM III (CLOSED) IN COMPLEX WITH MG UMPPNP
4brl LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM III (CLOSED) IN COMPLEX WITH TRANSITION STATE MIMI GUANOSINE 5'- PHOSPHOVANADATE
4brm SULFUR SAD PHASING OF THE LEGIONELLA PNEUMOPHILA NTPDASE1 - CRYSTAL FORM III (CLOSED) IN COMPLEX WITH SULFATE
4brn LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM III (CLOSED) IN COMPLEX WITH MG AMP
4bro LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM IV (PART- OPEN)
4brp LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM V (PART- OPEN)
4brq LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, IN COMPLEX WITH TWO PHOSPHATES BOUND TO ACTIVE SITE MG AND PRODUCT AMP