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(-) Description

Title :  P4 PROTEIN FROM BACTERIOPHAGE PHI12 S252A MUTANT IN COMPLEX WITH ADP
 
Authors :  D. E. Kainov, E. J. Mancini, J. Telenius, J. Lisal, J. M. Grimes, D. H. Bamford, D. I. Stuart, R. Tuma
Date :  21 Nov 07  (Deposition) - 04 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Non- Hydrolysable Atp Analogue, Hydrolase, Virus Dsrna, Molecular Motor, Packaging Atpase, Hexameric Helicase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. E. Kainov, E. J. Mancini, J. Telenius, J. Lisal, J. M. Grimes, D. H. Bamford, D. I. Stuart, R. Tuma
Structural Basis Of Mechanochemical Coupling In A Hexameric Molecular Motor.
J. Biol. Chem. V. 283 3607 2008
PubMed-ID: 18057007  |  Reference-DOI: 10.1074/JBC.M706366200

(-) Compounds

Molecule 1 - NTPASE P4
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPG27
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector: PET 32A
    Mutation: YES
    Organism Common: BACTERIOPHAGE PHI12
    Organism Scientific: PSEUDOMONAS PHAGE PHI12
    Organism Taxid: 161736
    Synonym: P4

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1ADP3Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1ADP6Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:133 , SER A:134 , GLY A:135 , LYS A:136 , THR A:137 , PRO A:138 , ASN A:234 , TYR A:288 , SER A:292 , HOH A:2295 , HOH A:2311 , HOH A:2312 , GLY C:276 , LEU C:277 , GLN C:278 , ARG C:279BINDING SITE FOR RESIDUE ADP A1301
2AC2SOFTWAREGLY A:276 , LEU A:277 , GLN A:278 , ARG A:279 , ASN B:133 , SER B:134 , GLY B:135 , LYS B:136 , THR B:137 , PRO B:138 , ASN B:234 , TYR B:288 , SER B:292 , HOH B:2282 , HOH B:2283 , HOH B:2285 , HOH B:2286 , HOH B:2287BINDING SITE FOR RESIDUE ADP B1301
3AC3SOFTWAREGLY B:276 , LEU B:277 , GLN B:278 , ARG B:279 , ASN C:133 , SER C:134 , GLY C:135 , LYS C:136 , THR C:137 , PRO C:138 , ASN C:234 , TYR C:288 , SER C:292 , HOH C:2291 , HOH C:2292 , HOH C:2293 , HOH C:2294 , HOH C:2295BINDING SITE FOR RESIDUE ADP C1301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VHJ)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asp A:189 -Ser A:190
2Asp B:189 -Ser B:190
3Asp C:189 -Ser C:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VHJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VHJ)

(-) Exons   (0, 0)

(no "Exon" information available for 2VHJ)

(-) 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:289
 aligned with Q94M05_9VIRU | Q94M05 from UniProtKB/TrEMBL  Length:331

    Alignment length:300
                                    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
         Q94M05_9VIRU     1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTSK 300
               SCOP domains d2vhja_ A: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2vhjA01 A:1-41,A:104-300                 --------------------------------------------------------------2vhjA01 A:1-41,A:104-300 P-loop containing nucleotide triphosphate hydrolases                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.......eeee.....eeee.....ee..eeeeeee.....eeeeeee..eeee...ee.............eeeee..eeee.eeeeee.....hhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhhhh.eeeee......-----------.hhhhhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhhhh.eeeee.....eeeeeee......eeeeeeeeee.hhh.eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vhj A   1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVI-----------ISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRANSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTSK 300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    |    -      |210       220       230       240       250       260       270       280       290       300
                                                                                                                                                                                                                            195         207                                                                                             


Chain B from PDB  Type:PROTEIN  Length:289
 aligned with Q94M05_9VIRU | Q94M05 from UniProtKB/TrEMBL  Length:331

    Alignment length:300
                                    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
         Q94M05_9VIRU     1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTSK 300
               SCOP domains d2vhjb_ B: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2vhjB01 B:1-41,B:104-300                 --------------------------------------------------------------2vhjB01 B:1-41,B:104-300 P-loop containing nucleotide triphosphate hydrolases                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.......eeee.....eeee.....ee..eeeeeee.....eeeeeee..eeee...ee.............eeeee..eeee.eeeeee.....hhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhh.eeeee......-----------.hhhhhhhhhhhhhhhhhhh.eeeee.........hhhhhhhhhhhh..eeeee.....eeeeeee......eeeeeeeeee.hhh.eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vhj B   1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVI-----------ISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRANSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTSK 300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    |    -      |210       220       230       240       250       260       270       280       290       300
                                                                                                                                                                                                                            195         207                                                                                             


Chain C from PDB  Type:PROTEIN  Length:289
 aligned with Q94M05_9VIRU | Q94M05 from UniProtKB/TrEMBL  Length:331

    Alignment length:300
                                    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
         Q94M05_9VIRU     1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTSK 300
               SCOP domains d2vhjc_ C: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2vhjC01 C:1-41,C:104-300                 --------------------------------------------------------------2vhjC01 C:1-41,C:104-300 P-loop containing nucleotide triphosphate hydrolases                                                                                                                         CATH domains
           Pfam domains (1) -NTPase_P4-2vhjC01 C:2-300                                                                                                                                                                                                                                                                                   Pfam domains (1)
           Pfam domains (2) -NTPase_P4-2vhjC02 C:2-300                                                                                                                                                                                                                                                                                   Pfam domains (2)
           Pfam domains (3) -NTPase_P4-2vhjC03 C:2-300                                                                                                                                                                                                                                                                                   Pfam domains (3)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......eeee.....eeee.........eeeeeee.....eeeeeee..eeee...ee.............eeeee..eeee.eeeeee.....hhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhh.eeeee......-----------.hhhhhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhhh..eeeee.....eeeeeee......eeeeeeeeee.hhh.eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vhj C   1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVI-----------ISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRANSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTSK 300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    |    -      |210       220       230       240       250       260       270       280       290       300
                                                                                                                                                                                                                            195         207
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: NTPase_P4] (12)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q94M05_9VIRU | Q94M05)
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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q94M05_9VIRU | Q94M05: 1w44 1w46 1w47 1w48 1w49 1w4a 1w4b 1w4c 2vhc 2vhq 2vht 2vhu 4blr 4bls 4blt

(-) Related Entries Specified in the PDB File

1w44 P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH ADP
1w46 P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH ADP AND MG
1w47 P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH ADP AND MN
1w48 P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH AMPCPP
1w49 P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH AMPCPP AND MG
1w4a P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH AMPCPP AND MN
1w4b P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH PRODUCT (AMPCPP MG 22C)
1w4c P4 PROTEIN FROM BACTERIOPHAGE PHI12 APO STATE
2vhc P4 PROTEIN FROM BACTERIOPHAGE PHI12 N234G MUTANT IN COMPLEX WITH AMPCPP AND MN