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(-) Description

Title :  F60M MUTANT, RIPA STRUCTURE
 
Authors :  R. Torres, C. W. Goulding
Date :  17 Oct 13  (Deposition) - 09 Apr 14  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Coenzyme A Transferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Torres, B. Lan, Y. Latif, N. Chim, C. W. Goulding
Structural Snapshots Along The Reaction Pathway Of Yersinia Pestis Ripa, A Putative Butyryl-Coa Transferase.
Acta Crystallogr. , Sect. D V. 70 1074 2014
PubMed-ID: 24699651  |  Reference-DOI: 10.1107/S1399004714000911

(-) Compounds

Molecule 1 - PUTATIVE 4-HYDROXYBUTYRATE COENZYME A TRANSFERASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ACH1, Y2385, YPO1926, YP_1668
    Mutation: YES
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 632
    Synonym: PUTATIVE COENZYME A TRANSFERASE, SIMILAR TO 4- HYDROXYBUTYRATE COA TRANSFERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric Unit (3, 19)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2COA2Ligand/IonCOENZYME A
3PO413Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2COA-1Ligand/IonCOENZYME A
3PO43Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2COA-1Ligand/IonCOENZYME A
3PO43Ligand/IonPHOSPHATE ION
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2COA1Ligand/IonCOENZYME A
3PO43Ligand/IonPHOSPHATE ION
Biological Unit 4 (3, 7)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2COA1Ligand/IonCOENZYME A
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:118 , GLU A:123 , HOH A:920 , HOH A:940 , HOH A:941 , HIS C:395 , ASN C:405BINDING SITE FOR RESIDUE PO4 A 501
02AC2SOFTWAREARG A:91 , ARG A:95BINDING SITE FOR RESIDUE PO4 A 502
03AC3SOFTWAREARG A:300 , HOH A:819 , HOH A:875 , HOH A:933 , HOH A:935 , HOH A:937 , HOH A:944 , LEU B:271 , ASP B:272 , PO4 B:503BINDING SITE FOR RESIDUE PO4 A 503
04AC4SOFTWAREGLU A:99 , SER C:23 , ILE C:52 , GLY C:53 , ARG C:78 , HOH C:907BINDING SITE FOR RESIDUE ACT A 504
05AC5SOFTWAREARG B:118 , GLU B:123 , HOH B:930 , HOH B:941 , HOH B:966 , HOH B:967 , HIS D:395 , ASN D:405BINDING SITE FOR RESIDUE PO4 B 501
06AC6SOFTWAREARG B:91 , ARG B:95BINDING SITE FOR RESIDUE PO4 B 502
07AC7SOFTWARELEU A:271 , ASP A:272 , PO4 A:503 , HOH A:944 , ARG B:300 , HOH B:602 , HOH B:607 , HOH B:774 , HOH B:843BINDING SITE FOR RESIDUE PO4 B 503
08AC8SOFTWAREGLU B:99 , SER D:23BINDING SITE FOR RESIDUE ACT B 504
09AC9SOFTWAREGLU C:61 , ALA C:88 , ARG C:91 , PRO C:198 , ARG C:200 , VAL C:227 , GLU C:249 , MET C:282 , GLU C:335 , GLN C:348 , HOH C:608 , HOH C:674 , HOH C:690 , HOH C:752 , HOH C:801 , HOH C:811 , HOH C:851 , HOH C:877BINDING SITE FOR RESIDUE COA C 501
10BC1SOFTWAREARG C:91 , ARG C:95 , HOH C:679 , HOH C:912BINDING SITE FOR RESIDUE PO4 C 502
11BC2SOFTWAREHIS A:395 , ASN A:405 , ARG C:118 , GLU C:123 , HOH C:602 , HOH C:606 , HOH C:711BINDING SITE FOR RESIDUE PO4 C 503
12BC3SOFTWAREASN C:112 , HIS C:114 , GLN C:115 , ASN C:306 , PRO C:308 , ASP C:350 , ARG C:353 , HOH C:716BINDING SITE FOR RESIDUE PO4 C 504
13BC4SOFTWAREGLU D:61 , THR D:87 , ALA D:88 , ARG D:91 , MET D:197 , PRO D:198 , ARG D:200 , VAL D:227 , GLU D:249 , MET D:282 , GLU D:335 , GLN D:348 , HOH D:681 , HOH D:683 , HOH D:755 , HOH D:759 , HOH D:768 , HOH D:813 , HOH D:845 , HOH D:868 , HOH D:899BINDING SITE FOR RESIDUE COA D 501
14BC5SOFTWARELYS B:373 , ARG D:91 , ARG D:95BINDING SITE FOR RESIDUE PO4 D 502
15BC6SOFTWAREHIS B:395 , ASN B:405 , ARG D:118 , GLU D:123 , HOH D:603 , HOH D:607 , HOH D:737BINDING SITE FOR RESIDUE PO4 D 503
16BC7SOFTWAREARG C:275 , ARG C:300 , HOH C:746 , ARG D:275 , ARG D:300 , HOH D:609 , HOH D:611 , HOH D:663 , HOH D:800 , HOH D:829BINDING SITE FOR RESIDUE PO4 D 504
17BC8SOFTWAREHOH B:684 , ASN D:112 , HIS D:114 , GLN D:115 , PRO D:308 , ASP D:350 , ARG D:353 , HOH D:608 , HOH D:669BINDING SITE FOR RESIDUE PO4 D 505
18BC9SOFTWAREHIS C:139 , HOH C:765 , TYR D:290BINDING SITE FOR RESIDUE ACT D 506
19CC1SOFTWARETYR C:290 , HIS D:139 , HIS D:180 , HOH D:769BINDING SITE FOR RESIDUE ACT D 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N8J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N8J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N8J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N8J)

(-) Exons   (0, 0)

(no "Exon" information available for 4N8J)

(-) 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:447
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.hhhhhhh......eeee.hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhh...hhhhh..eeeee...hhhhhhhhhhhhhh...........hhhhhhhhhhh.....eeeeee.......eee......hhhhhhhhh.eeeeee............eee.hhh.eeee...............hhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh...ee...eehhhhhhhhhh..............eee.ee..hhhhhhhh.....eee.hhhhhhhhhhhh....eeeeee..eee....ee............hhhhhhhhhhhhh...eeeee...ee....ee.ee...............eeee..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n8j A  -6 MGRGSEFMDIRALYDEKLTTPEEAVSSIASGSHLSMGMFAAEPPALLKALADRATRGDIGDLRVYYMETAKIAGDTILRYELNNRIKPYSMFVTAVERALIRRGIEDGGRKVVNYVPSNFHQAPRLLAEEIGIDTFMHTVSPMDCHGYFSLGVGNDYSSRIARSARRFIVEVNRYMPRVQGEAAAIHISEVDAIVENHVPLIEMPVRSAIPEYTSISHIIADLVPDGACLQMGVGALPNLVCGVLKDRNDLGIHTEVLNPGLVDLIRRGVVTNQRKTLDRGRSVFTFAMGQQEMYEYLNDHPAIFSRPVDYVNDPHIIAQNDNVVSINATLQIDLTGACNSEHMLGHQYSASGGQLDFVRGAYASKGGRSIIATPSTAAKGTVSRIIPRIDGPVTTPRIDTHYIVTEFGAVNLKGLSSTERALRIIELAHPDFRDELTQAAKKMHLI 440
                                     3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       


Chain B from PDB  Type:PROTEIN  Length:447
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.hhhhhhh......eeee.hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhh...hhhhh..eeeee...hhhhhhhhhhhhhh...........hhhhhhhhhhh.....eeeeee.......eee......hhhhhhhhh.eeeeee............eee.hhh.eeee..............hhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh...ee...eehhhhhhhhhh..............eee.ee..hhhhhhhhh....eee.hhhhhhhhhhhh....eeeeee..eee....ee............hhhhhhhhhhhhh...eeeee...ee....ee.ee...............eeee..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n8j B  -6 MGRGSEFMDIRALYDEKLTTPEEAVSSIASGSHLSMGMFAAEPPALLKALADRATRGDIGDLRVYYMETAKIAGDTILRYELNNRIKPYSMFVTAVERALIRRGIEDGGRKVVNYVPSNFHQAPRLLAEEIGIDTFMHTVSPMDCHGYFSLGVGNDYSSRIARSARRFIVEVNRYMPRVQGEAAAIHISEVDAIVENHVPLIEMPVRSAIPEYTSISHIIADLVPDGACLQMGVGALPNLVCGVLKDRNDLGIHTEVLNPGLVDLIRRGVVTNQRKTLDRGRSVFTFAMGQQEMYEYLNDHPAIFSRPVDYVNDPHIIAQNDNVVSINATLQIDLTGACNSEHMLGHQYSASGGQLDFVRGAYASKGGRSIIATPSTAAKGTVSRIIPRIDGPVTTPRIDTHYIVTEFGAVNLKGLSSTERALRIIELAHPDFRDELTQAAKKMHLI 440
                                     3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       


Chain C from PDB  Type:PROTEIN  Length:440
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhhh......eeee.hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhh...hhhhh..eeeee...hhhhhhhhhhhhhh......ee...hhhhhhhhhhh.....eeeeee.......eee......hhhhhhhhh.eeeeee.......ee...eee.hhh.eeee..............hhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh...ee...eehhhhhhhhhh..............eee.ee..hhhhhhhhh....eee.hhhhhhhhhhhh....eeeeee..eee....ee.............hhhhhhhhhhhh...eeeee...ee....ee.ee...............eeee..eeee....hhhhhhhhhhh..hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n8j C   1 MDIRALYDEKLTTPEEAVSSIASGSHLSMGMFAAEPPALLKALADRATRGDIGDLRVYYMETAKIAGDTILRYELNNRIKPYSMFVTAVERALIRRGIEDGGRKVVNYVPSNFHQAPRLLAEEIGIDTFMHTVSPMDCHGYFSLGVGNDYSSRIARSARRFIVEVNRYMPRVQGEAAAIHISEVDAIVENHVPLIEMPVRSAIPEYTSISHIIADLVPDGACLQMGVGALPNLVCGVLKDRNDLGIHTEVLNPGLVDLIRRGVVTNQRKTLDRGRSVFTFAMGQQEMYEYLNDHPAIFSRPVDYVNDPHIIAQNDNVVSINATLQIDLTGACNSEHMLGHQYSASGGQLDFVRGAYASKGGRSIIATPSTAAKGTVSRIIPRIDGPVTTPRIDTHYIVTEFGAVNLKGLSSTERALRIIELAHPDFRDELTQAAKKMHLI 440
                                    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       400       410       420       430       440


Chain D from PDB  Type:PROTEIN  Length:440
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhhh......eeee.hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhh...hhhhh..eeeee...hhhhhhhhhhhhhh......ee...hhhhhhhhhhh.....eeeeee.......eee......hhhhhhhhh.eeeeee............eee.hhh.eeee..............hhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh...ee...eehhhhhhhhhh..............eee.ee..hhhhhhhhh....eee.hhhhhhhhhhhh....eeeeee..eee....ee.............hhhhhhhhhhhh...eeeee...ee....ee.ee...............eeee..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n8j D   1 MDIRALYDEKLTTPEEAVSSIASGSHLSMGMFAAEPPALLKALADRATRGDIGDLRVYYMETAKIAGDTILRYELNNRIKPYSMFVTAVERALIRRGIEDGGRKVVNYVPSNFHQAPRLLAEEIGIDTFMHTVSPMDCHGYFSLGVGNDYSSRIARSARRFIVEVNRYMPRVQGEAAAIHISEVDAIVENHVPLIEMPVRSAIPEYTSISHIIADLVPDGACLQMGVGALPNLVCGVLKDRNDLGIHTEVLNPGLVDLIRRGVVTNQRKTLDRGRSVFTFAMGQQEMYEYLNDHPAIFSRPVDYVNDPHIIAQNDNVVSINATLQIDLTGACNSEHMLGHQYSASGGQLDFVRGAYASKGGRSIIATPSTAAKGTVSRIIPRIDGPVTTPRIDTHYIVTEFGAVNLKGLSSTERALRIIELAHPDFRDELTQAAKKMHLI 440
                                    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       400       410       420       430       440
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  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  (0, 0)

(no "SCOP Domain" information available for 4N8J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N8J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N8J)

(-) Gene Ontology  (5, 5)

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 Related Entries

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

UniProtKB/TrEMBL
        Q9ZC36_YERPE | Q9ZC36: 3qli 3qlk 3s8d 4n8h 4n8i 4n8k 4n8l

(-) Related Entries Specified in the PDB File

4n8h 4n8i 4n8k 4n8l