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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TRAFFIC ATPASE OF THE HELICOBACTER PYLORI TYPE IV SECRETION SYSTEM IN COMPLEX WITH ATPGAMMAS
 
Authors :  S. N. Savvides, H. J. Yeo, M. R. Beck, F. Blaesing, R. Lurz, E. Lanka, R. Bu W. Fischer, R. Haas, G. Waksman
Date :  08 Jan 03  (Deposition) - 06 May 03  (Release) - 07 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Virb11 Atpase, Bacterial Type Iv Secretion, Atpgammas, Hp0525, Helicobacter Pylori, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. N. Savvides, H. J. Yeo, M. R. Beck, F. Blaesing, R. Lurz, E. Lanka, R. Buhrdorf, W. Fischer, R. Haas, G. Waksman
Virb11 Atpases Are Dynamic Hexameric Assemblies: New Insights Into Bacterial Type Iv Secretion
Embo J. V. 22 1969 2003
PubMed-ID: 12727865  |  Reference-DOI: 10.1093/EMBOJ/CDG223

(-) Compounds

Molecule 1 - VIRB11 HOMOLOG
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HP0525
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: 26695

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 17)

Asymmetric Unit (5, 17)
No.NameCountTypeFull Name
12PE1Ligand/IonNONAETHYLENE GLYCOL
2AGS2Ligand/IonPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
3MG1Ligand/IonMAGNESIUM ION
4MSE12Mod. Amino AcidSELENOMETHIONINE
5SO41Ligand/IonSULFATE ION
Biological Unit 1 (4, 48)
No.NameCountTypeFull Name
12PE3Ligand/IonNONAETHYLENE GLYCOL
2AGS6Ligand/IonPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
3MG-1Ligand/IonMAGNESIUM ION
4MSE36Mod. Amino AcidSELENOMETHIONINE
5SO43Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:185 , AGS A:402 , HOH A:1022BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREASN A:61 , ARG A:113 , ARG A:133 , TYR A:140 , GLY A:179 , THR A:180 , GLY A:181 , SER A:182 , GLY A:183 , LYS A:184 , THR A:185 , THR A:186 , GLU A:248 , HIS A:273 , MG A:401 , HOH A:1002BINDING SITE FOR RESIDUE AGS A 402
3AC3SOFTWAREGLY B:181 , SER B:182 , GLY B:183 , LYS B:184 , THR B:185 , AGS B:402BINDING SITE FOR RESIDUE SO4 B 401
4AC4SOFTWAREASN B:61 , ARG B:133 , TYR B:140 , GLY B:179 , THR B:180 , GLY B:181 , SER B:182 , GLY B:183 , LYS B:184 , THR B:185 , THR B:186 , GLU B:248 , HIS B:273 , SO4 B:401 , HOH B:506BINDING SITE FOR RESIDUE AGS B 402
5AC5SOFTWAREASP A:38 , PHE A:39 , LYS A:41 , MSE A:42 , PRO A:67 , PHE A:68 , ASP A:69 , ARG A:73 , LYS B:41 , PHE B:68 , ASP B:69 , ARG B:73BINDING SITE FOR RESIDUE 2PE B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:119 -Pro A:120
2Ser B:119 -Pro B:120

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NLY)

(-) 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:323
 aligned with Q7BK04_HELPX | Q7BK04 from UniProtKB/TrEMBL  Length:330

    Alignment length:323
                                    15        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   
         Q7BK04_HELPX     6 LSAEDKKFLEVERALKEAALNPLRHATEELFGDFLKMENITEICYNGNKVVWVLKNNGEWQPFDVRDRKAFSLSRLMHFARCCASFKKKTIDNYENPILSSNLANGERVQIVLSPVTVNDETISISIRIPSKTTYPHSFFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTTYIKSIMEFIPKEERIISIEDTEEIVFKHHKNYTQLFFGGNITSADCLKSCLRMRPDRIILGELRSSEAYDFYNVLCSGHKGTLTTLHAGSSEEAFIRLANMSSSNSAARNIKFESLIEGFKDLIDMIVHINHHKQCDEFYIK 328
               SCOP domains d1nlya_ A: Hexameric traffic ATPase, HP0525                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------1nlyA01 A:25-135  [code=3.30.450.90, no name defined]                                                          1nlyA02 A:136-321 P-loop containing nucleotide triphosphate hydrolases                                                                                                                    ------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeeee...eeeeee....eeeee...hhhhhhhhhhhhhhhhhhhh..........eeeee.....eeeee...........eeeee.......hhhhhhhh.......hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh.....eeeee............eeeee.....hhhhhhhhhh.....eeeeee..hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhh....................eeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nly A   6 LSAEDKKFLEVERALKEAALNPLRHATEELFGDFLKmENITEICYNGNKVVWVLKNNGEWQPFDVRDRKAFSLSRLmHFARCCASFKKKTIDNYENPILSSNLANGERVQIVLSPVTVNDETISISIRIPSKTTYPHSFFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTTYIKSImEFIPKEERIISIEDTEEIVFKHHKNYTQLFFGGNITSADCLKSCLRmRPDRIILGELRSSEAYDFYNVLCSGHKGTLTTLHAGSSEEAFIRLANmSSSNSAARNIKFESLIEGFKDLIDmIVHINHHKQCDEFYIK 328
                                    15        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   
                                                               42-MSE                                  82-MSE                                                                                                       192-MSE                                        239-MSE                                         287-MSE                  312-MSE            


Chain B from PDB  Type:PROTEIN  Length:323
 aligned with Q7BK04_HELPX | Q7BK04 from UniProtKB/TrEMBL  Length:330

    Alignment length:323
                                    15        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   
         Q7BK04_HELPX     6 LSAEDKKFLEVERALKEAALNPLRHATEELFGDFLKMENITEICYNGNKVVWVLKNNGEWQPFDVRDRKAFSLSRLMHFARCCASFKKKTIDNYENPILSSNLANGERVQIVLSPVTVNDETISISIRIPSKTTYPHSFFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTTYIKSIMEFIPKEERIISIEDTEEIVFKHHKNYTQLFFGGNITSADCLKSCLRMRPDRIILGELRSSEAYDFYNVLCSGHKGTLTTLHAGSSEEAFIRLANMSSSNSAARNIKFESLIEGFKDLIDMIVHINHHKQCDEFYIK 328
               SCOP domains d1nlyb_ B: Hexameric traffic ATPase, HP0525                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------1nlyB01 B:25-135  [code=3.30.450.90, no name defined]                                                          1nlyB02 B:136-321 P-loop containing nucleotide triphosphate hydrolases                                                                                                                    ------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeeee...eeeeee....eeeee...hhhhhhhhhhhhhhhhhhhh..........eeeee.....eeeee...........eeeee.......hhhhhhhh.......hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh.....eeeee............eeeee.....hhhhhhhhhh.....eeeeee..hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhh....................eeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nly B   6 LSAEDKKFLEVERALKEAALNPLRHATEELFGDFLKmENITEICYNGNKVVWVLKNNGEWQPFDVRDRKAFSLSRLmHFARCCASFKKKTIDNYENPILSSNLANGERVQIVLSPVTVNDETISISIRIPSKTTYPHSFFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTTYIKSImEFIPKEERIISIEDTEEIVFKHHKNYTQLFFGGNITSADCLKSCLRmRPDRIILGELRSSEAYDFYNVLCSGHKGTLTTLHAGSSEEAFIRLANmSSSNSAARNIKFESLIEGFKDLIDmIVHINHHKQCDEFYIK 328
                                    15        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   
                                                               42-MSE                                  82-MSE                                                                                                       192-MSE                                        239-MSE                                         287-MSE                  312-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, 2)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1NLY)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q7BK04_HELPX | Q7BK04)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/TrEMBL
        Q7BK04_HELPX | Q7BK04: 1g6o 1nlz 1opx 2pt7

(-) Related Entries Specified in the PDB File

1g6o THE SAME PROTEIN (HP0525 FROM HELICOBACTER PYLORI) COMPLEXED WITH ADP