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(-) Description

Title :  CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, ASP11ASN MUTANT
 
Authors :  Y. Patskovsky, H. Huang, R. Toro, J. A. Gerlt, S. K. Burley, D. Dunaway-M S. C. Almo, New York Sgx Research Center For Structural Genomi (Nysgxrc), Enzyme Function Initiative (Efi)
Date :  23 Feb 11  (Deposition) - 27 Apr 11  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.24
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Pyrophosphatase, Magnesium Bin New York Sgx Research Center For Structural Genomics, Enzyme Function Initiative, Efi, Psi-2, Protein Structure Initiative, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Huang, Y. Patskovsky, R. Toro, J. D. Farelli, C. Pandya, S. C. Almo, K. N. Allen, D. Dunaway-Mariano
Divergence Of Structure And Function In The Haloacid Dehalogenase Enzyme Superfamily: Bacteroides Thetaiotaomicron Bt2127 Is An Inorganic Pyrophosphatase.
Biochemistry V. 50 8937 2011
PubMed-ID: 21894910  |  Reference-DOI: 10.1021/BI201181Q

(-) Compounds

Molecule 1 - INORGANIC PYROPHOSPHATASE
    Chains: A, B
    EC Number: 3.6.1.1
    Engineered: YES
    Gene: BT_2127
    Mutation: YES
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 818

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:79 , GLN A:117BINDING SITE FOR RESIDUE CL A 225
2AC2SOFTWAREMET A:20 , PRO A:21 , SER A:24 , HOH A:266BINDING SITE FOR RESIDUE CL A 226
3AC3SOFTWARELYS B:79 , GLN B:117 , HOH B:349BINDING SITE FOR RESIDUE CL B 225
4AC4SOFTWAREARG B:40 , HOH B:232BINDING SITE FOR RESIDUE CL B 226
5AC5SOFTWAREPRO B:21 , TYR B:44 , HOH B:251 , HOH B:522BINDING SITE FOR RESIDUE CL B 227

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QU5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:147 -Pro A:148
2Lys B:147 -Pro B:148

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QU5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QU5)

(-) Exons   (0, 0)

(no "Exon" information available for 3QU5)

(-) 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:221
 aligned with Q8A5V9_BACTN | Q8A5V9 from UniProtKB/TrEMBL  Length:224

    Alignment length:221
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 
         Q8A5V9_BACTN     4 KLKAVLFDMDGVLFNSMPYHSEAWHQVMKTHGLDLSREEAYMHEGRTGASTINIVFQRELGKEATQEEIESIYHEKSILFNSYPEAERMPGAWELLQKVKSEGLTPMVVTGSGQLSLLERLEHNFPGMFHKELMVTAFDVKYGKPNPEPYLMALKKGGLKADEAVVIENAPLGVEAGHKAGIFTIAVNTGPLDGQVLLDAGADLLFPSMQTLCDSWDTIML 224
               SCOP domains d3qu5a_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee........hhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh..eeeee....hhhhhhhhhhhh....hhh.eehhhhh......hhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhh..eeeee.....hhhhhhhh...eee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qu5 A   4 KLKAVLFNMDGVLFNSMPYHSEAWHQVMKTHGLDLSREEAYMHEGRTGASTINIVFQRELGKEATQEEIESIYHEKSILFNSYPEAERMPGAWELLQKVKSEGLTPMVVTGSGQLSLLERLEHNFPGMFHKELMVTAFDVKYGKPNPEPYLMALKKGGLKADEAVVIENAPLGVEAGHKAGIFTIAVNTGPLDGQVLLDAGADLLFPSMQTLCDSWDTIML 224
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 


Chain B from PDB  Type:PROTEIN  Length:229
 aligned with Q8A5V9_BACTN | Q8A5V9 from UniProtKB/TrEMBL  Length:224

    Alignment length:229
                                 1                                                                                                                                                                                                                               
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215         
         Q8A5V9_BACTN     - -----MRKKLKAVLFDMDGVLFNSMPYHSEAWHQVMKTHGLDLSREEAYMHEGRTGASTINIVFQRELGKEATQEEIESIYHEKSILFNSYPEAERMPGAWELLQKVKSEGLTPMVVTGSGQLSLLERLEHNFPGMFHKELMVTAFDVKYGKPNPEPYLMALKKGGLKADEAVVIENAPLGVEAGHKAGIFTIAVNTGPLDGQVLLDAGADLLFPSMQTLCDSWDTIML 224
               SCOP domains d3qu5b_ B: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------HAD_2-3qu5B01 B:8-190                                                                                                                                                                  ---------------------------------- Pfam domains (1)
           Pfam domains (2) ------------HAD_2-3qu5B02 B:8-190                                                                                                                                                                  ---------------------------------- Pfam domains (2)
         Sec.struct. author .....hhhhh.eeee........hhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh..eeeee....hhhhhhhhhhhh....hhh.eehhhhh......hhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh..eeeee.....hhhhhhhh...eee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qu5 B  -4 PRGSHMRKKLKAVLFNMDGVLFNSMPYHSEAWHQVMKTHGLDLSREEAYMHEGRTGASTINIVFQRELGKEATQEEIESIYHEKSILFNSYPEAERMPGAWELLQKVKSEGLTPMVVTGSGQLSLLERLEHNFPGMFHKELMVTAFDVKYGKPNPEPYLMALKKGGLKADEAVVIENAPLGVEAGHKAGIFTIAVNTGPLDGQVLLDAGADLLFPSMQTLCDSWDTIML 224
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215
   Legend:   → Mismatch (orange background)
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  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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QU5)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8A5V9_BACTN | Q8A5V9)
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.
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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 Related Entries

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

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        Q8A5V9_BACTN | Q8A5V9: 3qu2 3qu4 3qu7 3qu9 3qub 3quc 3quq 3qut 3qx7 3qxg 3qyp 3r9k

(-) Related Entries Specified in the PDB File

3qu2 CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, A CLOSED CAP CONFORMATION, WILD-TYPE PROTEIN
3qu4 CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, ASP13ALA MUTANT
3qu7 CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, ASP13ASN MUTANT COMPLEXED WITH CALCIUM AND PHOSPHATE
3qu9 CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, ASP13ASN MUTANT COMPLEXED WITH MAGNESIUM AND TARTRATE
3qub CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, GLU47ALA MUTANT COMPLEXED WITH SULFATE
3quc CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, GLU47ASN MUTANT COMPLEXED WITH SULFATE
3quq CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, AN OPEN CAP CONFORMATION, WILD-TYPE PROTEIN
3qut CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, ASP13ASN MUTANT, AN OPEN CAP CONFORMATION
3qx7 CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON COMPLEXED WITH PHOSPHATE, A CLOSED CAP CONFORMATION, WILD-TYPE PROTEIN
3qxg CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON COMPLEXED WITH CALCIUM, A CLOSED CAP CONFORMATION, WILD-TYPE PROTEIN
3qyp CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON, GLU47ASN MUTANT COMPLEXED WITH CALCIUM AND PHOSPHATE
3r9k CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON COMPLEXED WITH CALCIUM, GLU47ASP MUTANT COMPLEXED WITH SULFATE, A CLOSED CAP CONFORMATION