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(-) Description

Title :  P4 PROTEIN FROM BACTERIOPHAGE PHI12 Q278A MUTANT IN COMPLEX WITH AMPCPP
 
Authors :  K. El Omari, C. Meier, D. Kainov, G. Sutton, J. M. Grimes, M. M. Poranen, D. H. Bamford, R. Tuma, D. I. Stuart, E. J. Mancini
Date :  04 May 13  (Deposition) - 21 Aug 13  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Hydrolase, Packaging, Cystoviridae (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. El Omari, C. Meier, D. Kainov, G. Sutton, J. M. Grimes, M. M. Poranen D. H. Bamford, R. Tuma, D. I. Stuart, E. J. Mancini
Tracking In Atomic Detail The Functional Specializations In Viral Reca Helicases That Occur During Evolution.
Nucleic Acids Res. V. 41 9396 2013
PubMed-ID: 23939620  |  Reference-DOI: 10.1093/NAR/GKT713

(-) Compounds

Molecule 1 - NTPASE P4
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Common: BACTERIOPHAGE PHI12
    Organism Scientific: PSEUDOMONAS PHAGE PHI12
    Organism Taxid: 161736

 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
1APC3Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1APC6Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:133 , GLY A:135 , LYS A:136 , THR A:137 , GLU A:160 , LYS A:192 , ASN A:234 , TYR A:288 , SER A:292 , SER C:252 , ARG C:272 , GLY C:276 , ASN C:318BINDING SITE FOR RESIDUE APC A 400
2AC2SOFTWARESER A:252 , ARG A:272 , GLY A:276 , ARG A:279 , ASN A:318 , ASN B:133 , GLY B:135 , LYS B:136 , THR B:137 , PRO B:138 , GLU B:160 , LYS B:192 , ASN B:234 , TYR B:288 , SER B:292BINDING SITE FOR RESIDUE APC B 400
3AC3SOFTWARESER B:252 , ARG B:272 , GLY B:276 , ASN B:318 , GLY C:135 , LYS C:136 , THR C:137 , GLU C:160 , ASN C:234 , TYR C:288 , SER C:292BINDING SITE FOR RESIDUE APC C 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BLS)

(-) 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 4BLS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BLS)

(-) Exons   (0, 0)

(no "Exon" information available for 4BLS)

(-) 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:302
 aligned with Q94M05_9VIRU | Q94M05 from UniProtKB/TrEMBL  Length:331

    Alignment length:326
                                    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      
         Q94M05_9VIRU     1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTSKQSGGKQASGKAIQTVIKNDELESVLR 326
               SCOP domains d4blsa_ A: automated matches                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......eeee.....eeee.........eeeeeee.....eeeeeee..eeee...ee.............eeeee..eeee.eeeeee.....hhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhhhh.eeeee......-----------.hhhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhhh...eeeee......eeeeee......eeeeee.eee.hhh.eee...-------------.eeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bls A   1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVI-----------ISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLARLTHTLQTSYGEHSVLTIHTS-------------QTVIKNDELESVLR 326
                                    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        |-         -  |    320      
                                                                                                                                                                                                                            195         207                                                                                         299           313             


Chain B from PDB  Type:PROTEIN  Length:303
 aligned with Q94M05_9VIRU | Q94M05 from UniProtKB/TrEMBL  Length:331

    Alignment length:327
                                    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       
         Q94M05_9VIRU     1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTSKQSGGKQASGKAIQTVIKNDELESVLRR 327
               SCOP domains d4blsb_ B: automated matches                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......eeee.....eeee.........eeeeeee.....eeeeeee..eeee...ee.............eeeee..eeee.eeeeee.....hhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhh.eeeee......-----------.hhhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhhh...eeeee......eeeeee......eeeeee.eee.hhh.eee...-------------.eeehhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bls B   1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVI-----------ISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLARLTHTLQTSYGEHSVLTIHTS-------------QTVIKNDELESVLRR 327
                                    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        |-         -  |    320       
                                                                                                                                                                                                                            195         207                                                                                         299           313              


Chain C from PDB  Type:PROTEIN  Length:302
 aligned with Q94M05_9VIRU | Q94M05 from UniProtKB/TrEMBL  Length:331

    Alignment length:327
                                    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       
         Q94M05_9VIRU     1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTSKQSGGKQASGKAIQTVIKNDELESVLRR 327
               SCOP domains d4blsc_ C: automated matches                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......eeee.....eeee.........eeeeeee.....eeeeeee..eeee...ee.............eeeee..eeee.eeeeee.....hhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhh.eeeee......-----------.hhhhhhhhhhhhhhhhhhh.eeeee...-..hhhhhhhhhhhhhh...eeeee......eeeeee......eeeeee.eee.hhh.eee...-------------.eeehhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bls C   1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVI-----------ISRGAFDLLSDIGAMAASRGCVVIASLNP-SNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLARLTHTLQTSYGEHSVLTIHTS-------------QTVIKNDELESVLRR 327
                                    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        |-         -  |    320       
                                                                                                                                                                                                                            195         207                         235 |                                                           299           313              
                                                                                                                                                                                                                                                                      237
   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  (0, 0)

(no "CATH Domain" information available for 4BLS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BLS)

(-) 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 2vhj 2vhq 2vht 2vhu 4blr 4blt

(-) Related Entries Specified in the PDB File

4blo P4 PROTEIN FROM BACTERIOPHAGE PHI6 IN COMPLEX WITH ADP
4blp P4 PROTEIN FROM BACTERIOPHAGE PHI13
4blq P4 PROTEIN FROM BACTERIOPHAGE PHI8
4blr P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH UTP
4blt P4 PROTEIN FROM BACTERIOPHAGE PHI12 S292A MUTANT IN COMPLEX WITH AMPCPP
4bwy P4 PROTEIN FROM BACTERIOPHAGE PHI8 (R32)