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(-) Description

Title :  CRYSTAL STRUCTURE OF A PHOSPHONATE MONOESTER HYDROLASE FROM RHIZOBIUM LEGUMINOSARUM: A NEW MEMBER OF THE ALKALINE PHOSPHATASE SUPERFAMILY
 
Authors :  S. Jonas, M. Hyvonen, F. Hollfelder
Date :  18 Mar 08  (Deposition) - 30 Sep 08  (Release) - 16 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.42
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Phosphonate Monoester Hydrolase, Hydrolase, Plasmid, Formylglycine, Phosphodiesterase, Alkaline Phosphatase Superfamily (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Jonas, B. Van Loo, M. Hyvonen, F. Hollfelder
A New Member Of The Alkaline Phosphatase Superfamily With A Formylglycine Nucleophile: Structural And Kinetic Characterisation Of A Phosphonate Monoester Hydrolase/Phosphodiesterase From Rhizobium Leguminosarum.
J. Mol. Biol. V. 384 120 2008
PubMed-ID: 18793651  |  Reference-DOI: 10.1016/J.JMB.2008.08.072

(-) Compounds

Molecule 1 - PUTATIVE SULFATASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 TUNER
    Expression System Taxid: 511693
    Expression System Vector: PASK-IBA5PLUS
    Organism Scientific: RHIZOBIUM LEGUMINOSARUM BV. VICIAE
    Organism Taxid: 216596
    Strain: 3841
    Synonym: PHOSPHONATE MONOESTER HYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric Unit (5, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CA1Ligand/IonCALCIUM ION
3DDZ1Mod. Amino Acid3,3-DIHYDROXY L-ALANINE
4MN1Ligand/IonMANGANESE (II) ION
5NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1ACT8Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3DDZ4Mod. Amino Acid3,3-DIHYDROXY L-ALANINE
4MN-1Ligand/IonMANGANESE (II) ION
5NA-1Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:12 , CYS A:57 , DDZ A:57 , ASP A:324 , HIS A:325BINDING SITE FOR RESIDUE MN A1515
2AC2SOFTWAREASP A:12 , CYS A:57 , DDZ A:57 , ASP A:324 , HIS A:325BINDING SITE FOR RESIDUE CA A1516
3AC3SOFTWAREHOH A:2035 , HOH A:2042 , HOH A:2151 , HOH A:2271 , HOH A:2588 , HOH A:2596BINDING SITE FOR RESIDUE NA A1518
4AC4SOFTWAREARG A:444 , TYR A:445 , ASP A:459 , ARG A:461 , HOH A:2255BINDING SITE FOR RESIDUE ACT A1517
5AC5SOFTWARETYR A:105 , THR A:106 , THR A:107 , GLY A:126 , ASP A:127 , LEU A:128 , HOH A:2169BINDING SITE FOR RESIDUE ACT A1519

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VQR)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Val A:55 -Pro A:56
2Arg A:216 -Pro A:217
3Pro A:219 -Pro A:220
4Ala A:225 -Pro A:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VQR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VQR)

(-) Exons   (0, 0)

(no "Exon" information available for 2VQR)

(-) 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:514
 aligned with Q1M964_RHIL3 | Q1M964 from UniProtKB/TrEMBL  Length:514

    Alignment length:514
                                                                                   57                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
                                                                                 56 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
                                    11        21        31        41        51    | | 60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510    
         Q1M964_RHIL3     2 RKKNVLLIVVDQWRADFVPHVLRADGKIDFLKTPNLDRLCREGVTFRNHVTTCVP-CGPARASLLTGLYLMNHRAVQNTVPLDQRHLNLGKALRGVGYDPALIGYTTTVPDPRTTSPNDPRFRVLGDLMDGFHPVGAFEPNMEGYFGWVAQNGFDLPEHRPDIWLPEGEDAVAGATDRPSRIPKEFSDSTFFTERALTYLKGRDGKPFFLHLGYYRPHPPFVASAPYHAMYRPEDMPAPIRAANPDIEAAQHPLMKFYVDSIRRGSFFQGAEGSGATLDEAELRQMRATYCGLITEVDDCLGRVFSYLDETGQWDDTLIIFTSDHGEQLGDHHLLGKIGYNDPSFRIPLVIKDAGENARAGAIESGFTESIDVMPTILDWLGGKIPHACDGLSLLPFLSEGRPQDWRTELHYEYDFRDVYYSEPQSFLGLGMNDCSLCVIQDERYKYVHFAALPPLFFDLRHDPNEFTNLADDPAYAALVRDYAQKALSWRLKHADRTLTHYRSGPEGLSERSH 514
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --Sulfatase-2vqrA01 A:4-469                                                                                                                                                                                                                                                                                                                                                                                                                                                          --------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.......hhhhhhhh.......hhhhhhhhhhheeeeeee.......hhhhhhhhhh.hhhhhh.............hhhhhhhh....eeeee..............hhhhh.........eeeee.hhhhhhhhhhhhhh......hhhhhhh.................hhhhhhhhhhhhhhhhhhhhhh....eeeee............hhhhh.hhhhh.......hhhhhhh.hhhhhhhhhhh.hhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee......hhhhh......hhhhhh..eeee..........eeeeeee..hhhhhhhhhh............hhhhhh..........eeeeee........hhhhhh.hhhh.eeeeee...eeeeee.....eeee.............hhhhhhhhhhhhhhhhhhhhhh.......ee......ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vqr A   2 RKKNVLLIVVDQWRADFVPHVLRADGKIDFLKTPNLDRLCREGVTFRNHVTTCVPaCGPARASLLTGLYLMNHRAVQNTVPLDQRHLNLGKALRGVGYDPALIGYTTTVPDPRTTSPNDPRFRVLGDLMDGFHPVGAFEPNMEGYFGWVAQNGFDLPEHRPDIWLPEGEDAVAGATDRPSRIPKEFSDSTFFTERALTYLKGRDGKPFFLHLGYYRPHPPFVASAPYHAMYRPEDMPAPIRAANPDIEAAQHPLMKFYVDSIRRGSFFQGAEGSGATLDEAELRQMRATYCGLITEVDDCLGRVFSYLDETGQWDDTLIIFTSDHGEQLGDHHLLGKIGYNDPSFRIPLVIKDAGENARAGAIESGFTESIDVMPTILDWLGGKIPHACDGLSLLPFLSEGRPQDWRTELHYEYDFRDVYYSEPQSFLGLGMNDCSLCVIQDERYKYVHFAALPPLFFDLRHDPNEFTNLADDPAYAALVRDYAQKALSWRLKHADRTLTHYRSGPEGLSERSH 514
                                    11        21        31        41        51     |  60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510    
                                                                                  57-DDZ
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2VQR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VQR)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Alk_phosphatase (47)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q1M964_RHIL3 | Q1M964)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008484    sulfuric ester hydrolase activity    Catalysis of the reaction: RSO-R' + H2O = RSOOH + R'H. This reaction is the hydrolysis of any sulfuric ester bond, any ester formed from sulfuric acid, O=SO(OH)2.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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  2vqr
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