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(-) Description

Title :  CRYSTAL STRUCTURE OF BACTERIAL ATP SULFURYLASE FROM THE RIFTIA PACHYPTILA SYMBIONT
 
Authors :  J. D. Beynon, I. J. Macrae, S. L. Huston, D. C. Nelson, I. H. Segel, A. J. Fisher
Date :  27 Jun 01  (Deposition) - 07 Dec 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Adenylyl Transferase, Sulfurylase, Aps, Chemoautotroph, Bromide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. Beynon, I. J. Macrae, S. L. Huston, D. C. Nelson, I. H. Segel, A. J. Fisher
Crystal Structure Of Atp Sulfurylase From The Bacterial Symbiont Of The Hydrothermal Vent Tubeworm Riftia Pachyptila.
Biochemistry V. 40 14509 2001
PubMed-ID: 11724564  |  Reference-DOI: 10.1021/BI015643L
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SULFATE ADENYLYLTRANSFERASE
    Chains: A
    EC Number: 2.7.7.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SULFUR-OXIDIZING ENDOSYMBIONT OF RIFTIA PACHYPTILA
    Organism Taxid: 35843
    Synonym: CHEMOAUTOTROPIC BACTERIAL ATP SULFURYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1BR8Ligand/IonBROMIDE ION
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2SO46Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:7 , ASP A:8 , GLU A:9 , LYS A:11BINDING SITE FOR RESIDUE SO4 A 1001
02AC2SOFTWARESER A:193 , HOH A:3363 , HOH A:3382 , HOH A:3498BINDING SITE FOR RESIDUE BR A 2004
03AC3SOFTWAREGLU A:9 , LEU A:10 , HOH A:3085 , HOH A:3331BINDING SITE FOR RESIDUE BR A 2005
04AC4SOFTWAREASN A:202 , HIS A:205 , HIS A:208 , GLY A:361 , ARG A:365 , HOH A:3078 , HOH A:3129 , HOH A:3173BINDING SITE FOR RESIDUE SO4 A 1002
05AC5SOFTWAREPRO A:18 , ALA A:240BINDING SITE FOR RESIDUE BR A 2006
06AC6SOFTWARESER A:38 , GLN A:39 , HOH A:3043 , HOH A:3074BINDING SITE FOR RESIDUE BR A 2007
07AC7SOFTWAREGLN A:199 , ARG A:201BINDING SITE FOR RESIDUE BR A 2008
08AC8SOFTWAREALA A:207 , HIS A:208 , HIS A:332 , THR A:333 , HOH A:3046 , HOH A:3078 , HOH A:3152 , HOH A:3345 , HOH A:3422BINDING SITE FOR RESIDUE SO4 A 1003
09AC9SOFTWAREHIS A:205 , SER A:379BINDING SITE FOR RESIDUE BR A 2001
10BC1SOFTWAREPHE A:173 , PRO A:174 , ASP A:175 , THR A:176BINDING SITE FOR RESIDUE BR A 2002
11BC2SOFTWAREGLY A:295 , ARG A:296 , ASP A:331 , HOH A:3251 , HOH A:3422BINDING SITE FOR RESIDUE BR A 2003

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:53 -Pro A:54

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1JHD)

(-) 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:396
 aligned with SAT_RIFPS | Q54506 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:396
                                                                                  55                      78                                                                                                                                                                                                                                                                                       359                                  
                                                                                54 |                    77 |                                                                                                                                                                                                                                                                                     358 |                                  
                                    10        20        30        40        50   | |  59        69       |78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358 |     367       377       387      
            SAT_RIFPS     1 MIKPVGSDELKPLFVYDPEEHHKLSHEAESLPSVVISSQGPRVSSMMGAGYFSP-AGFMNVADAMGAAEKMTLSDGSS-SCSVLCLLENTDAIGDAKRIALRDPNVEGNPVLAVMDIEAIEEVSDEQMAVMTDKVYRTTDMDHIGVKTFNSQGRVAVSGPIQVLNFSYFQADFPDTFRTAVEIRNEIKEHGWSKVVAFQTRNPMHRAHEELCRMPMESLDADGVVVHMLLGKLKKGDIPAPVRDAAIRTMAEVYFPPNTVMVTGYGFDMLYAGPREAVLHAYFRQNMGATHFIIGREPPAWVTTTVPSTPRPSSMTKCQRAPWRSRSSCRPHGLLQEAEQDCDDARRAGSHQGRLRTALR-HQGREMLGQGIAPPPEFSRPEVAKILMDLLPVHQQ 393
               SCOP domains d1jhda1 A:1-173 ATP sulfurylase N-terminal domain                                                                                                                            d1jhda2 A:174-396 ATP sulfurylase catalytic domain                                                                                                                                                                              SCOP domains
               CATH domains 1jhdA02 A:1-193 Sulfate adenylyltransferase                                                                                                                                                      1jhdA01 A:194-396 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                     CATH domains
               Pfam domains -PUA_2-1jhdA02 A:2-166                                                                                                                                                ------ATP-sulfurylase-1jhdA01 A:173-389                                                                                                                                                                                        ------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhh...eee.hhhhhhhhhhhhh.......ee.hhhhhhhhhhhh..............ee..........eeeee........eeeeee..eeee.hhhhhhhhhhhhhh.....hhhhhhhh....eeeeeeeee..hhhhhhhh.....hhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhhhh....eeeeeee......hhhhhhhhhhhhhhh...eeee.............hhhhhhhhhh........eeee...eeee....eeee.hhh...hhh.ee..hhhhhhhhhhh.........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jhd A   1 MIKPVGSDELKPLFVYDPEEHHKLSHEAESLPSVVISSQAAGNAVMMGAGYFSPLQGFMNVADAMGAAEKMTLSDGSFFPVPVLCLLENTDAIGDAKRIALRDPNVEGNPVLAVMDIEAIEEVSDEQMAVMTDKVYRTTDMDHIGVKTFNSQGRVAVSGPIQVLNFSYFQADFPDTFRTAVEIRNEIKEHGWSKVVAFQTRNPMHRAHEELCRMAMESLDADGVVVHMLLGKLKKGDIPAPVRDAAIRTMAEVYFPPNTVMVTGYGFDMLYAGPREAVLHAYFRQNMGATHFIIGRDHAGVGDYYGAFDAQTIFDDEVPEGAMEIEIFRADHTAYSKKLNKIVMMRDVPDHTKEDFVLLSGTKVREMLGQGIAPPPEFSRPEVAKILMDYYQSINS 396
                                    10        20        30        40        50        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
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (SAT_RIFPS | Q54506)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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.
biological process
    GO:0070814    hydrogen sulfide biosynthetic process    The chemical reactions and pathways resulting in the formation of hydrogen sulfide, H2S.
    GO:0000103    sulfate assimilation    The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.

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