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(-) Description

Title :  CRYSTAL STRUCTURE OF ATP SULFURYLASE FROM THERMUS THERMOPHILLUS HB8 IN COMPLEX WITH APS
 
Authors :  Y. Taguchi, M. Sugishima, K. Fukuyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  11 Nov 03  (Deposition) - 06 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Product Binding Complex, Zinc, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Taguchi, M. Sugishima, K. Fukuyama
Crystal Structure Of A Novel Zinc-Binding Atp Sulfurylase From Thermus Thermophilus Hb8
Biochemistry V. 43 4111 2004
PubMed-ID: 15065853  |  Reference-DOI: 10.1021/BI036052T
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ATP SULFURYLASE
    Chains: A, B
    EC Number: 2.7.7.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1ADX2Ligand/IonADENOSINE-5'-PHOSPHOSULFATE
2CL5Ligand/IonCHLORIDE ION
3NA4Ligand/IonSODIUM ION
4ZN2Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:294 , CYS A:297 , CYS A:306 , HIS A:310BINDING SITE FOR RESIDUE ZN A 601
02AC2SOFTWARECYS B:294 , CYS B:297 , CYS B:306 , HIS B:310BINDING SITE FOR RESIDUE ZN B 602
03AC3SOFTWAREARG A:164 , LYS A:195 , GLY A:263BINDING SITE FOR RESIDUE CL A 602
04AC4SOFTWARETHR A:109BINDING SITE FOR RESIDUE NA A 603
05AC5SOFTWAREGLU A:96BINDING SITE FOR RESIDUE NA A 604
06AC6SOFTWAREGLU A:219BINDING SITE FOR RESIDUE NA A 605
07AC7SOFTWAREHOH A:726BINDING SITE FOR RESIDUE CL A 606
08AC8SOFTWAREARG A:277BINDING SITE FOR RESIDUE CL A 608
09AC9SOFTWAREPHE A:161 , GLN A:162 , THR A:163 , ARG A:164 , ASN A:165 , HIS A:168 , ALA A:170 , HIS A:171 , MET A:230 , GLY A:256 , ARG A:257 , HIS A:259 , ALA A:260 , GLY A:289 , VAL A:291 , ILE A:317 , HOH A:609BINDING SITE FOR RESIDUE ADX A 564
10BC1SOFTWAREPHE B:161 , GLN B:162 , THR B:163 , ARG B:164 , HIS B:168 , ALA B:170 , HIS B:171 , LEU B:174 , MET B:230 , GLY B:256 , ARG B:257 , HIS B:259 , ALA B:260 , GLY B:289 , VAL B:291 , ILE B:317BINDING SITE FOR RESIDUE ADX B 574

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V47)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:27 -Pro A:28
2Phe B:27 -Pro B:28

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V47)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V47)

(-) Exons   (0, 0)

(no "Exon" information available for 1V47)

(-) 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:346
 aligned with Q5SKH7_THET8 | Q5SKH7 from UniProtKB/TrEMBL  Length:349

    Alignment length:346
                                    13        23        33        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      
         Q5SKH7_THET8     4 TLPALEIGEDERLDLENLATGAFFPVKGFMTREEALSVAHEMRLPTGEVWTIPILLQFREKPRVGPGNTVALLHGGERVALLHVAEAYELDLEALARAVFGTDSETHPGVARLYGKGPYALAGRVEVLKPRPRTPLEKTPEEVRAFFRQRGWRKVVAFQTRNAPHRAHEYLIRLGLELADGVLVHPILGAKKPDDFPTEVIVEAYQALIRDFLPQERVAFFGLATPMRYAGPKEAVFHALVRKNFGATHFLVGRDHAGVGDFYDPYAAHRIFDRLPPLGIEIVKVGAVFHCPLCGGIASERTCPEGHREKRTAISMTKVRALLREGKAPPSELVRPELLPILRRGV 349
               SCOP domains d1v47a1 A:4-135 ATP sulfurylase N-terminal domain                                                                                   d1v47a2 A:136-349 ATP sulfurylase catalytic domain                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------1v47A02 A:137-349 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhhhhh..........hhhhhhhhhhhh.............eee..........eeeeee..eeeeeee..eeee.hhhhhhhhhhh.....hhhhhhhhhh..eeee..eee...........hhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhh.eeeeee..........hhhhhhhhhhhhhhhhhhhh.eee..........hhhhhhhhhhhhhhh...eeee.............hhhhhhhhhh.....eeee...eeee....eeee....hhhhhhhhee.hhhhhhhhhhh.........hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v47 A   4 TLPALEIGEDERLDLENLATGAFFPVKGFMTREEALSVAHEMRLPTGEVWTIPILLQFREKPRVGPGNTVALLHGGERVALLHVAEAYELDLEALARAVFGTDSETHPGVARLYGKGPYALAGRVEVLKPRPRTPLEKTPEEVRAFFRQRGWRKVVAFQTRNAPHRAHEYLIRLGLELADGVLVHPILGAKKPDDFPTEVIVEAYQALIRDFLPQERVAFFGLATPMRYAGPKEAVFHALVRKNFGATHFLVGRDHAGVGDFYDPYAAHRIFDRLPPLGIEIVKVGAVFHCPLCGGIASERTCPEGHREKRTAISMTKVRALLREGKAPPSELVRPELLPILRRGV 349
                                    13        23        33        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      


Chain B from PDB  Type:PROTEIN  Length:343
 aligned with Q5SKH7_THET8 | Q5SKH7 from UniProtKB/TrEMBL  Length:349

    Alignment length:344
                                    13        23        33        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    
         Q5SKH7_THET8     4 TLPALEIGEDERLDLENLATGAFFPVKGFMTREEALSVAHEMRLPTGEVWTIPILLQFREKPRVGPGNTVALLHGGERVALLHVAEAYELDLEALARAVFGTDSETHPGVARLYGKGPYALAGRVEVLKPRPRTPLEKTPEEVRAFFRQRGWRKVVAFQTRNAPHRAHEYLIRLGLELADGVLVHPILGAKKPDDFPTEVIVEAYQALIRDFLPQERVAFFGLATPMRYAGPKEAVFHALVRKNFGATHFLVGRDHAGVGDFYDPYAAHRIFDRLPPLGIEIVKVGAVFHCPLCGGIASERTCPEGHREKRTAISMTKVRALLREGKAPPSELVRPELLPILRR 347
               SCOP domains d1v47b1 B:4-135 ATP sulfurylase N-terminal domain                                                                                   d1v47b2 B:136-347 ATP sulfurylase catalytic domain                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------1v47B02 B:137-347 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                             CATH domains
           Pfam domains (1) PUA_2-1v47B03 B:4-133                                                                                                             ---ATP-sulfurylase-1v47B01 B:137-347                                                                                                                                                                                   Pfam domains (1)
           Pfam domains (2) PUA_2-1v47B04 B:4-133                                                                                                             ---ATP-sulfurylase-1v47B02 B:137-347                                                                                                                                                                                   Pfam domains (2)
         Sec.struct. author ...eee.hhhhhhhhhhhhh..........hhhhhhhhhhhh.............eee..........eeeee....eeeeee..eeee.hhhhhhhhhh......hhhhhhhhh...eeee..eee...........hhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhh.eeeeee..........hhhhhhhhhhhhhhhhhhhh.eee..........hhhhhhhhhhhhhhh...eeee.............hhhhhhhhhh.....eeee...eeee....eeee....hhhhhhhhee.hhhhhhh..-..........hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v47 B   4 TLPALEIGEDERLDLENLATGAFFPVKGFMTREEALSVAHEMRLPTGEVWTIPILLQFREKPRVGPGNTVALLHGGERVALLHVAEAYELDLEALARAVFGTDSETHPGVARLYGKGPYALAGRVEVLKPRPRTPLEKTPEEVRAFFRQRGWRKVVAFQTRNAPHRAHEYLIRLGLELADGVLVHPILGAKKPDDFPTEVIVEAYQALIRDFLPQERVAFFGLATPMRYAGPKEAVFHALVRKNFGATHFLVGRDHAGVGDFYDPYAAHRIFDRLPPLGIEIVKVGAVFHCPLCGGIASERTCPEGHREKRTAISMTKVRALL-EGKAPPSELVRPELLPILRR 347
                                    13        23        33        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    
                                                                                                                                                                                                                                                                                                                                                            326 |                   
                                                                                                                                                                                                                                                                                                                                                              328
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)
(-)
Clan: PUA (42)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5SKH7_THET8 | Q5SKH7)
molecular function
    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.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0004781    sulfate adenylyltransferase (ATP) activity    Catalysis of the reaction: ATP + sulfate = diphosphate + adenylylsulfate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.

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