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(-) Description

Title :  CRYSTAL STRUCTURE OF A GTP-REGULATED ATP SULFURYLASE HETERODIMER FROM PSEUDOMONAS SYRINGAE
 
Authors :  J. D. Mougous, D. H. Lee, S. C. Hubbard, M. W. Schelle, D. J. Vocadlo, J. M. Berger, C. R. Bertozzi
Date :  31 May 05  (Deposition) - 17 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Barrel, Switch Domain, Heterodimer, Pyrophosphate, G Protein, Gtpase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. Mougous, D. H. Lee, S. C. Hubbard, M. W. Schelle, D. J. Vocadlo, J. M. Berger, C. R. Bertozzi
Molecular Basis For G Protein Control Of The Prokaryotic Atp Sulfurylase.
Mol. Cell V. 21 109 2006
PubMed-ID: 16387658  |  Reference-DOI: 10.1016/J.MOLCEL.2005.10.034
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SULFATE ADENYLYLTRANSFERASE SUBUNIT 2
    Chains: A
    EC Number: 2.7.7.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET28B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: CYSD
    Organism Scientific: PSEUDOMONAS SYRINGAE
    Organism Taxid: 317
    Synonym: SULFATE ADENYLATE TRANSFERASE, SAT, ATP- SULFURYLASE SMALL SUBUNIT, ATP SULFURYLASE CATALYTIC SUBUNIT (CYSD)
 
Molecule 2 - SULFATE ADENYLATE TRANSFERASE, SUBUNIT 1/ADENYLYLSULFATE KINASE
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET21A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: CYSNC
    Organism Scientific: PSEUDOMONAS SYRINGAE PV. TOMATO STR. DC3000
    Organism Taxid: 223283
    Synonym: GTPASE DOMAIN OF ATP SULFURYLASE REGULATORY SUBUNIT (CYSN)

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 24)

Asymmetric/Biological Unit (5, 24)
No.NameCountTypeFull Name
1AGS1Ligand/IonPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION
4MSE20Mod. Amino AcidSELENOMETHIONINE
5NA1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:211 , AGS A:600 , HOH A:708 , HOH A:714BINDING SITE FOR RESIDUE MG A 598
2AC2SOFTWAREASP A:38 , GLU A:138 , AGS A:600BINDING SITE FOR RESIDUE NA A 700
3AC3SOFTWAREASN B:32 , ASP B:34 , ASP B:35 , GLY B:36 , LYS B:37 , SER B:38 , THR B:39 , GLN B:83 , ASN B:165 , LYS B:166 , ASP B:168 , LEU B:169 , SER B:204 , ALA B:205 , LEU B:206 , ASN B:257 , HOH B:624BINDING SITE FOR RESIDUE GDP B 599
4AC4SOFTWARELEU A:32 , TYR A:33 , SER A:34 , GLY A:36 , LYS A:37 , ASP A:38 , SER A:39 , MSE A:60 , HIS A:61 , VAL A:62 , LYS A:114 , GLY A:133 , GLU A:138 , ALA A:210 , ALA A:211 , MG A:598 , NA A:700 , HOH A:708BINDING SITE FOR RESIDUE AGS A 600

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:51 -Pro A:52

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ZUN)

(-) 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:204
 aligned with CYSD_PSESM | Q87WW0 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:218
                                   1                                                                                                                                                                                                                  
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203        
           CYSD_PSESM     - -------MVDKLTHLKQLEAESIHIIREVAAEFDNPVMLYSIGKDSAVMLHLARKAFFPGKLPFPVMHVDTRWKFQEMYRFRDQMVEEMGLDLITHINPDGVAQGINPFTHGSAKHTDIMKTEGLKQALDKHGFDAAFGGARRDEEKSRAKERVYSFRDSKHRWDPKNQRPELWNVYNGNVNKGESIRVFPLSNWTELDIWQYIYLEGIPIVPLYFAA 211
               SCOP domains -------d1zuna1 A:1-211 Sulfate adenylyltransferase subunit 2, CysD                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------PAPS_reduct-1zunA01 A:28-211                                                                                                                                                             Pfam domains
         Sec.struct. author ....hhhhh...hhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhh....eeee..--------------.hhhhhhhhhhhhhhhhhhhh..eee.......hhhhhhh..eeee......hhhhh................eeee......hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zun A  -6 LVPRGSHmVDKLTHLKQLEAESIHIIREVAAEFDNPVmLYSIGKDSAVmLHLARKAFFPGKLPFPVmHVDTRWKFQEmYRFRDQmVEEmGLDLITHIN--------------SAKHTDImKTEGLKQALDKHGFDAAFGGARRDEEKSRAKERVYSFRDSKHRWDPKNQRPELWNVYNGNVNKGESIRVFPLSNWTELDIWQYIYLEGIPIVPLYFAA 211
                                   | 3        13        23       |33        43        53      | 63       |73    |   83       | -         -  |    113       123       133       143       153       163       173       183       193       203        
                                   1-MSE                        31-MSE     42-MSE            60-MSE     71-MSE 78-MSE       91            106      |                                                                                                  
                                                                                                                   82-MSE                        113-MSE                                                                                              


Chain B from PDB  Type:PROTEIN  Length:394
 aligned with Q87WW1_PSESM | Q87WW1 from UniProtKB/TrEMBL  Length:632

    Alignment length:419
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425         
         Q87WW1_PSESM    16 LGQHERKEMLRFLTCGNVDDGKSTLIGRLLHDSKMIYEDHLEAITRDSKKSGTTGDDVDLALLVDGLQAEREQGITIDVAYRYFSTAKRKFIIADTPGHEQYTRNMATGASTCDLAIILVDARYGVQTQTRRHSYIASLLGIKHIVVAINKMDLNGFDERVFESIKADYLKFAEGIAFKPTTMAFVPMSALKGDNVVNKSERSPWYAGQSLMEILETVEIASDRNYTDLRFPVQYVNRPNLNFRGFAGTLASGIVHKGDEIVVLPSGKSSRVKSIVTFEGELEQAGPGQAVTLTMEDEIDISRGDLLVHADNVPQVSDAFDAMLVWMAEEPMLPGKKYDIKRATSYVPGSIASITHRVDVNTLEEGPASSLQLNEIGRVKVSLDAPIALDGYSSNRTTGAFIVIDRLTNGTVAAGMIIA 434
               SCOP domains d1zunb3 B:16-237 Sulfate adenylate t                  ran  sferase su     bunit cysN/C, EF-Tu domain G-like domain                                                                                                            d1zunb1 B:238-329 Sulfate adenylate transferase subunit cysN/C, EF-Tu domain 2-like domain  d1zunb2 B:330-434 Sulfate adenylate transferase subunit cysN/C, EF-Tu domain 3-like domain                SCOP domains
               CATH domains 1zunB01 B:16-238 P-loop containing n                  ucl  eotide tri     phosphate hydrolases                                                                                                                                 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------GTP_EFTU-1zunB01 B:22-258                                                                                                                                                                                                                    --GTP_EFTU_D2-1zunB02 B:261-323                                  --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee.....hhhhhhhhhhhhh...------------------..h--hhhhhhhhhh-----.....eeeeee...eeeeeee...hhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhh......eeeeee........................hhhhhhh...........eee..eee.......eeeee.....ee...eeee.....eeeeeeeee..eee.ee....eeeeee..........eeee......eeeeeeeeeee...........eeee....eeeeeeeeeeeee.................eeeeeeeeeeeee...........eeeee......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zun B  16 LGQHERKEmLRFLTCGNVDDGKSTLIGRLLHDSKmI------------------GDD--LALLVDGLQA-----ITIDVAYRYFSTAKRKFIIADTPGHEQYTRNmATGASTCDLAIILVDARYGVQTQTRRHSYIASLLGIKHIVVAINKmDLNGFDERVFESIKADYLKFAEGIAFKPTTmAFVPmSALKGDNVVNKSERSPWYAGQSLmEILETVEIASDRNYTDLRFPVQYVNRPNLNFRGFAGTLASGIVHKGDEIVVLPSGKSSRVKSIVTFEGELEQAGPGQAVTLTmEDEIDISRGDLLVHADNVPQVSDAFDAmLVWmAEEPmLPGKKYDIKRATSYVPGSIASITHRVDVNTLEEGPASSLQLNEIGRVKVSLDAPIALDGYSSNRTTGAFIVIDRLTNGTVAAGmIIA 434
                                    25        35        45    ||   -         -    | | 75        |-    |   95       105       115     | 125       135       145       155       165 |     175       185       195  |    205       215       225 |     235       245       255       265       275       285       295       305    |  315       325       335  |   |345 |     355       365       375       385       395       405       415       425     |   
                                   24-MSE                    50-MSE              70 | 75       84    90                            121-MSE                                       167-MSE                        198-MSE|                     227-MSE                                                                            310-MSE                     338-MSE    |                                                                                 431-MSE
                                                              51                   72                                                                                                                                203-MSE                                                                                                                                    342-MSE|                                                                                       
                                                                                                                                                                                                                                                                                                                                                                     347-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  (4, 4)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)
(-)
Clan: P-loop_NTPase (1112)
(-)
Clan: no clan defined [family: GTP_EFTU_D2] (39)

(-) Gene Ontology  (16, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CYSD_PSESM | Q87WW0)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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: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.
    GO:0000103    sulfate assimilation    The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
    GO:0019419    sulfate reduction    The chemical reactions and pathways resulting in the reduction of sulfate to another sulfur-containing ion or compound such as hydrogen sulfide, adenosine-phosphosulfate (APS) or thiosulfate.
    GO:0006790    sulfur compound metabolic process    The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.

Chain B   (Q87WW1_PSESM | Q87WW1)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0004020    adenylylsulfate kinase activity    Catalysis of the reaction: ATP + adenylylsulfate = ADP + 3'-phosphoadenosine 5'-phosphosulfate.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0000103    sulfate assimilation    The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
    GO:0006790    sulfur compound metabolic process    The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.

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 Related Entries

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