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(-) Description

Title :  LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH MG AND THIAMINE PHOSPHOVANADATE
 
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 :  1.69
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  (6, 11)

Asymmetric/Biological Unit (6, 11)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2DVT2Ligand/IonDECAVANADATE
3GOL1Ligand/IonGLYCEROL
4MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5MG2Ligand/IonMAGNESIUM ION
6TMV2Ligand/IonTHIAMINE-PHOSPHOVANADATE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY 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:188 , GLY A:189 , ALA A:190 , SER A:191 , GLN A:231 , ASN A:302 , TYR A:346 , TYR A:350 , MG A:1396 , DVT A:1398 , HOH A:2007 , HOH A:2008 , HOH A:2020 , HOH A:2108 , HOH A:2109 , HOH A:2117BINDING SITE FOR RESIDUE TMV A1395
02AC2SOFTWARETMV A:1395 , HOH A:2007 , HOH A:2008 , HOH A:2109 , HOH A:2117BINDING SITE FOR RESIDUE MG A1396
03AC3SOFTWAREPHE A:226 , VAL A:275 , HIS A:276 , LYS A:277 , GLN A:281 , HOH A:2139 , HOH A:2248 , GLU B:267BINDING SITE FOR RESIDUE MES A1397
04AC4SOFTWARELYS A:80 , LYS A:82 , ASN A:302 , PRO A:378 , TMV A:1395 , HOH A:2021 , HOH A:2022BINDING SITE FOR RESIDUE DVT A1398
05AC5SOFTWAREGLY 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:188 , GLY B:189 , ALA B:190 , SER B:191 , GLN B:231 , GLY B:299 , ASN B:302 , TYR B:346 , TYR B:350 , MG B:1396 , DVT B:1398 , HOH B:2005 , HOH B:2006 , HOH B:2018 , HOH B:2092 , HOH B:2093 , HOH B:2098 , HOH B:2115 , HOH B:2176BINDING SITE FOR RESIDUE TMV B1395
06AC6SOFTWARETMV B:1395 , HOH B:2005 , HOH B:2006 , HOH B:2093 , HOH B:2098BINDING SITE FOR RESIDUE MG B1396
07AC7SOFTWARESER A:241 , GLU A:267 , HOH A:2156 , HIS B:224 , SER B:225 , PHE B:226 , VAL B:275 , HIS B:276 , GLN B:281BINDING SITE FOR RESIDUE MES B1397
08AC8SOFTWARELYS B:80 , LYS B:82 , ASN B:302 , PRO B:378 , TMV B:1395 , HOH B:2019 , HOH B:2041 , HOH B:2150BINDING SITE FOR RESIDUE DVT B1398
09AC9SOFTWAREMET A:34 , HIS B:42 , SER B:61 , TYR B:62 , ASP B:63 , HIS B:72 , GLU B:74BINDING SITE FOR RESIDUE GOL B1399
10BC1SOFTWAREARG A:122 , GLY A:156 , HOH A:2074 , ASN B:240 , ASP B:253BINDING SITE FOR RESIDUE CL B1400
11BC2SOFTWAREASN A:240 , ASP A:253 , HOH A:2170 , ARG B:122 , GLY B:156BINDING SITE FOR RESIDUE CL A1399

(-) 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 4BRH)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4BRH)

(-) 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:361
 aligned with Q5ZUA2_LEGPH | Q5ZUA2 from UniProtKB/TrEMBL  Length:393

    Alignment length:361
                                                                                                                                                                                                                                                                                                                                                                                                 393 
                                    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       393 
         Q5ZUA2_LEGPH    34 ADTNPCEKHSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELEYWFRQQSQWQLAEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHRA-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.eeeeeeee....eeeeeeeeee.....eeeeeeeeeeee..hhhhh..hhhhhhhhhhhhhh.......eeeeeehhhhhh.hhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhhh..........eeeeee...eeeeeee.......hhh.eeeeee..eeeeeeeeeee..hhhhhhh....hhhhh..............hhhhhhhhhhhhhhh..hhhhhhhhhhhhh...eeeeeehhhhhhh.........eehhhhhhhhhhhhh...hhhhhhhhh....hhhhhhhhhhhhhhhhh..........eee.hhhhh..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4brh A  34 MDTNPCEKHSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELDYWFRQQSQWQLVEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHRAL 394
                                    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       393 


Chain B from PDB  Type:PROTEIN  Length:359
 aligned with Q5ZUA2_LEGPH | Q5ZUA2 from UniProtKB/TrEMBL  Length:393

    Alignment length:359
                                                                                                                                                                                                                                                                                                                                                                                               393 
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       | 
         Q5ZUA2_LEGPH    36 TNPCEKHSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELEYWFRQQSQWQLAEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHRA-   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.eeeeeeee....eeeeeeeeee.....eeeeeeeeeeee..hhhhh..hhhhhhhhhhhhhh......eeeeeeehhhhhh.hhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhhhh..........eeeeee...eeeeeee.......hhh.eeeeee..eeeeeeeeeee..hhhhhhh....hhhhh..............hhhhhhhhhhhhhhh..hhhhhhhhhhhhh...eeeeeehhhhhhh.........eeehhhhhhhhhhhh...hhhhhhhhh....hhhhhhhhhhhhhhhhh.........eeee.hhhhh..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4brh B  36 TNPCEKHSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELDYWFRQQSQWQLVEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHRAL 394
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385
   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 4BRH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4brg 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 CA AMPNP
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, AMPNP COMPLEX
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
4brg LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH MG GMPPNP
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