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(-) Description

Title :  STRUCTURE OF A HAM1 PROTEIN FROM COXIELLA BURNETII
 
Authors :  J. Cheung, M. C. Franklin, M. Rudolph, M. Cassidy, E. Gary, F. Burshteyn
Date :  09 Sep 11  (Deposition) - 21 Sep 11  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Ham1 Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Franklin, J. Cheung, M. J. Rudolph, F. Burshteyn, M. Cassidy, E. Gary, B. Hillerich, Z. K. Yao, P. R. Carlier, M. Totrov, J. D. Love
Structural Genomics For Drug Design Against The Pathogen Coxiella Burnetii.
Proteins V. 83 2124 2015
PubMed-ID: 26033498  |  Reference-DOI: 10.1002/PROT.24841

(-) Compounds

Molecule 1 - NON-CANONICAL PURINE NTP PYROPHOSPHATASE
    Chains: A, B, C, D
    EC Number: 3.6.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CBU_0043
    Organism Scientific: COXIELLA BURNETII
    Organism Taxid: 227377
    Strain: RSA493
    Synonym: NON-STANDARD PURINE NTP PYROPHOSPHATASE, NUCLEOSIDE- TRIPHOSPHATE DIPHOSPHATASE, NUCLEOSIDE-TRIPHOSPHATE PYROPHOSPHATASE, NTPASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1CA5Ligand/IonCALCIUM ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:41 , ASP A:69 , HOH A:215 , HOH A:245 , HOH A:421 , HOH A:449 , HOH A:934BINDING SITE FOR RESIDUE CA A 201
2AC2SOFTWAREGLU B:41 , ASP B:69 , HOH B:839 , HOH B:1011 , HOH B:1212BINDING SITE FOR RESIDUE CA B 201
3AC3SOFTWARESER B:70 , PHE B:118 , HIS B:182 , HOH B:222BINDING SITE FOR RESIDUE EDO B 202
4AC4SOFTWAREGLU C:41 , ASP C:69 , HOH C:835 , HOH C:1012BINDING SITE FOR RESIDUE CA C 201
5AC5SOFTWAREGLU D:41 , ASP D:69 , HOH D:247 , HOH D:397 , HOH D:573 , HOH D:890BINDING SITE FOR RESIDUE CA D 201
6AC6SOFTWAREHOH C:907 , HOH C:1107 , HOH D:215 , HOH D:242 , HOH D:682BINDING SITE FOR RESIDUE CA D 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:80 -Pro A:81
2Ala B:80 -Pro B:81
3Ala C:80 -Pro C:81
4Ala D:80 -Pro D:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TQU)

(-) 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:197
 aligned with IXTPA_COXBU | Q83FA3 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       
          IXTPA_COXBU     1 MLEIVLASQNSSKLAEMQELLRDLEIKFIPQTEFSVPDIEETGSTFVENAIIKARHAAKQTGLPALADDSGLTIAALNSAPGVFSSRYAGKNATDAERIQKVLEALEAADDSDRSASFHCVIALMENENDPAPLICHGVWEGEIAREPRGKNGFGYDPIFYVPSHQRTAAELDPQEKNAISHRGQALEQLSTVLTEA 197
               SCOP domains d3tqua_ A: automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhh....eeeee.hhhh.........hhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhh..hhhhh........hhhhhhhhhhhhhhhhh....eeeeeeeeeee........eeeeeeeeeee...........hhh.ee...........hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tqu A   1 mLEIVLASQNSSKLAEmQELLRDLEIKFIPQTEFSVPDIEETGSTFVENAIIKARHAAKQTGLPALADDSGLTIAALNSAPGVFSSRYAGKNATDAERIQKVLEALEAADDSDRSASFHCVIALmENENDPAPLICHGVWEGEIAREPRGKNGFGYDPIFYVPSHQRTAAELDPQEKNAISHRGQALEQLSTVLTEA 197
                            |       10      | 20        30        40        50        60        70        80        90       100       110       120    |  130       140       150       160       170       180       190       
                            |              17-MSE                                                                                                     125-MSE                                                                    
                            1-MSE                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:197
 aligned with IXTPA_COXBU | Q83FA3 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       
          IXTPA_COXBU     1 MLEIVLASQNSSKLAEMQELLRDLEIKFIPQTEFSVPDIEETGSTFVENAIIKARHAAKQTGLPALADDSGLTIAALNSAPGVFSSRYAGKNATDAERIQKVLEALEAADDSDRSASFHCVIALMENENDPAPLICHGVWEGEIAREPRGKNGFGYDPIFYVPSHQRTAAELDPQEKNAISHRGQALEQLSTVLTEA 197
               SCOP domains d3tqub_ B: automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhh....eeeee.hhhh.........hhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhh..hhhhh........hhhhhhhhhhhhhhhhh....eeeeeeeeeee........eeeeeeeeeee...........hhh.ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tqu B   1 mLEIVLASQNSSKLAEmQELLRDLEIKFIPQTEFSVPDIEETGSTFVENAIIKARHAAKQTGLPALADDSGLTIAALNSAPGVFSSRYAGKNATDAERIQKVLEALEAADDSDRSASFHCVIALmENENDPAPLICHGVWEGEIAREPRGKNGFGYDPIFYVPSHQRTAAELDPQEKNAISHRGQALEQLSTVLTEA 197
                            |       10      | 20        30        40        50        60        70        80        90       100       110       120    |  130       140       150       160       170       180       190       
                            1-MSE          17-MSE                                                                                                     125-MSE                                                                    


Chain C from PDB  Type:PROTEIN  Length:197
 aligned with IXTPA_COXBU | Q83FA3 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       
          IXTPA_COXBU     1 MLEIVLASQNSSKLAEMQELLRDLEIKFIPQTEFSVPDIEETGSTFVENAIIKARHAAKQTGLPALADDSGLTIAALNSAPGVFSSRYAGKNATDAERIQKVLEALEAADDSDRSASFHCVIALMENENDPAPLICHGVWEGEIAREPRGKNGFGYDPIFYVPSHQRTAAELDPQEKNAISHRGQALEQLSTVLTEA 197
               SCOP domains d3tquc_ C: automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhh....eeeee.hhhh.........hhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhh..hhhhh........hhhhhhhhhhhhhhhhh....eeeeeeeeeee........eeeeeeeeeee...........hhh.eee....ee....hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tqu C   1 mLEIVLASQNSSKLAEmQELLRDLEIKFIPQTEFSVPDIEETGSTFVENAIIKARHAAKQTGLPALADDSGLTIAALNSAPGVFSSRYAGKNATDAERIQKVLEALEAADDSDRSASFHCVIALmENENDPAPLICHGVWEGEIAREPRGKNGFGYDPIFYVPSHQRTAAELDPQEKNAISHRGQALEQLSTVLTEA 197
                            |       10      | 20        30        40        50        60        70        80        90       100       110       120    |  130       140       150       160       170       180       190       
                            1-MSE          17-MSE                                                                                                     125-MSE                                                                    


Chain D from PDB  Type:PROTEIN  Length:197
 aligned with IXTPA_COXBU | Q83FA3 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       
          IXTPA_COXBU     1 MLEIVLASQNSSKLAEMQELLRDLEIKFIPQTEFSVPDIEETGSTFVENAIIKARHAAKQTGLPALADDSGLTIAALNSAPGVFSSRYAGKNATDAERIQKVLEALEAADDSDRSASFHCVIALMENENDPAPLICHGVWEGEIAREPRGKNGFGYDPIFYVPSHQRTAAELDPQEKNAISHRGQALEQLSTVLTEA 197
               SCOP domains d3tqud_ D: automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhh....eeeee.hhhh.........hhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhh..hhhhh........hhhhhhhhhhhhhhhhh....eeeeeeeeeee........eeeeeeeeeee...........hhh.ee...........hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tqu D   1 mLEIVLASQNSSKLAEmQELLRDLEIKFIPQTEFSVPDIEETGSTFVENAIIKARHAAKQTGLPALADDSGLTIAALNSAPGVFSSRYAGKNATDAERIQKVLEALEAADDSDRSASFHCVIALmENENDPAPLICHGVWEGEIAREPRGKNGFGYDPIFYVPSHQRTAAELDPQEKNAISHRGQALEQLSTVLTEA 197
                            |       10      | 20        30        40        50        60        70        80        90       100       110       120    |  130       140       150       160       170       180       190       
                            1-MSE          17-MSE                                                                                                     125-MSE
   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  (1, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TQU)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (IXTPA_COXBU | Q83FA3)
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:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    GO:0017111    nucleoside-triphosphatase activity    Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
    GO:0047429    nucleoside-triphosphate diphosphatase activity    Catalysis of the reaction: H2O + a nucleoside triphosphate = diphosphate + a nucleotide.
    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.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0009143    nucleoside triphosphate catabolic process    The chemical reactions and pathways resulting in the breakdown of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
    GO:0009117    nucleotide metabolic process    The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
    GO:0006163    purine nucleotide metabolic process    The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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