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(-) Description

Title :  RESORUFIN LIGASE WITH BOUND RESORUFIN-AMP ANALOG
 
Authors :  P. J. Goldman, C. L. Drennan
Date :  28 Jun 14  (Deposition) - 22 Oct 14  (Release) - 05 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.51
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 :  E. Coli Lpla, Computational Enzyme Design (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. S. Liu, L. G. Nivon, F. Richter, P. J. Goldman, T. J. Deerinck, J. Z. Yao, D. Richardson, W. S. Phipps, A. Z. Ye, M. H. Ellisman, C. L. Drennan, D. Baker, A. Y. Ting
Computational Design Of A Red Fluorophore Ligase For Site-Specific Protein Labeling In Living Cells.
Proc. Natl. Acad. Sci. Usa V. 111 E4551 2014
PubMed-ID: 25313043  |  Reference-DOI: 10.1073/PNAS.1404736111

(-) Compounds

Molecule 1 - LIPOATE-PROTEIN LIGASE A
    Chains: A, B, C, D
    EC Number: 2.7.7.63
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES
    Gene: LPLA
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: DH5A
    Synonym: LIPOATE-PROTEIN LIGASE

 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  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
137P4Ligand/Ion5'-O-{[5-(7-HYDROXY-3-OXO-3H-PHENOXAZIN-2-YL)PENTANOYL]SULFAMOYL}ADENOSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
137P1Ligand/Ion5'-O-{[5-(7-HYDROXY-3-OXO-3H-PHENOXAZIN-2-YL)PENTANOYL]SULFAMOYL}ADENOSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
137P1Ligand/Ion5'-O-{[5-(7-HYDROXY-3-OXO-3H-PHENOXAZIN-2-YL)PENTANOYL]SULFAMOYL}ADENOSINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
137P1Ligand/Ion5'-O-{[5-(7-HYDROXY-3-OXO-3H-PHENOXAZIN-2-YL)PENTANOYL]SULFAMOYL}ADENOSINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
137P1Ligand/Ion5'-O-{[5-(7-HYDROXY-3-OXO-3H-PHENOXAZIN-2-YL)PENTANOYL]SULFAMOYL}ADENOSINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:20 , TRP A:37 , ARG A:70 , SER A:72 , GLY A:75 , ALA A:76 , VAL A:77 , PHE A:78 , HIS A:79 , ASN A:83 , LYS A:133 , SER A:137 , ALA A:138 , ARG A:140 , GLY A:149 , THR A:151 , LEU A:161 , LEU A:165 , SER A:179 , VAL A:180 , SER A:182binding site for residue 37P A 401
2AC2SOFTWAREALA B:20 , ARG B:70 , GLY B:75 , ALA B:76 , VAL B:77 , PHE B:78 , HIS B:79 , ASN B:83 , LYS B:133 , GLY B:136 , SER B:137 , ALA B:138 , ARG B:140 , GLY B:149 , THR B:151 , LEU B:153 , LEU B:161 , LEU B:165 , SER B:179 , VAL B:180 , ARG B:181 , SER B:182 , VAL B:184binding site for residue 37P B 401
3AC3SOFTWAREALA C:20 , TRP C:37 , ARG C:70 , SER C:72 , GLY C:75 , VAL C:77 , PHE C:78 , HIS C:79 , ASN C:83 , THR C:87 , LYS C:133 , GLY C:136 , SER C:137 , ALA C:138 , GLY C:149 , THR C:151 , LEU C:153 , LEU C:161 , SER C:179 , VAL C:180 , ARG C:181 , SER C:182binding site for residue 37P C 401
4AC4SOFTWARELEU D:17 , ALA D:20 , TRP D:37 , ARG D:70 , SER D:72 , GLY D:75 , ALA D:76 , VAL D:77 , PHE D:78 , HIS D:79 , ASN D:83 , ASN D:121 , LYS D:133 , SER D:137 , ALA D:138 , GLY D:149 , THR D:151 , LEU D:153 , LEU D:161 , LEU D:165 , SER D:179 , VAL D:180 , ARG D:181 , SER D:182 , VAL D:184binding site for residue 37P D 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:92 -Pro A:93
2Lys B:92 -Pro B:93
3Lys C:92 -Pro C:93
4Lys D:92 -Pro D:93

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4TVW)

(-) 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:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhh....eeeeeee...eeee....hhhhhhhhhhhhhh..eeee.......eee....eeeeeeee....hhhhhhhhhhhhhhhhh..eeee...eeeeee..eeeeee.eeeee...eeeeee......hhhhhhhhh.....eeee...........hhhhh....hhhhhhhhhhhhhhhhhh.....eee.........hhhhhhhhhhhhhhhh.....eeeeeeeee..eeeeeeeeee..eeeeeeeee....hhhhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tvw A   1 STLRLLISDSYDPWFNLAVAECIFRQMPATQRVLFLWRNADTVVIGRAQNPWKECNTRRMEEDNVRLARRSSGGGAVFHDLGNTCFTFMAGKPEYDKTISTSIVLNALNALGVSAEASGRNDLVVKTVEGDRKVSGSAYRETKDRGAHGGTLLLNADLSRLANYLNPDKKKLAAKGITSVRSRVTNLTELLPGITHEQVCEAITEAFFAHYGERVEAEIISPNKTPDLPNFAETFARQSSWEWNFGQAPAFSHLLDERFTWGGVELHFDVEKGHITRAQVFTDSLNPAPLEALAGRLQGCLYRADMLQQECEALLVDFPEQEKELRELSAWMAGAVR 337
                                    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       


Chain B from PDB  Type:PROTEIN  Length:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhh....eeeeeee...eeee....hhhhhhhhhhhhhh..eeee.......eee....eeeeeeee....hhhhhhhhhhhhhhh....ee......eeeee..eeeeee.eeeee...eeeeee......hhhhhhhhh.....eeee...........hhhhh....hhhhhhhhhhhhhhhhhh.....eee.........hhhhhhhhhhhhhhhh.....eeeeeeeee..eeeeeeeeee..eeeeeeeee....hhhhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tvw B   1 STLRLLISDSYDPWFNLAVAECIFRQMPATQRVLFLWRNADTVVIGRAQNPWKECNTRRMEEDNVRLARRSSGGGAVFHDLGNTCFTFMAGKPEYDKTISTSIVLNALNALGVSAEASGRNDLVVKTVEGDRKVSGSAYRETKDRGAHGGTLLLNADLSRLANYLNPDKKKLAAKGITSVRSRVTNLTELLPGITHEQVCEAITEAFFAHYGERVEAEIISPNKTPDLPNFAETFARQSSWEWNFGQAPAFSHLLDERFTWGGVELHFDVEKGHITRAQVFTDSLNPAPLEALAGRLQGCLYRADMLQQECEALLVDFPEQEKELRELSAWMAGAVR 337
                                    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       


Chain C from PDB  Type:PROTEIN  Length:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhh....eeeeeee...eeee....hhhhhhhhhhhhhh..eeee.......eee....eeeeeeee....hhhhhhhhhhhhhhh.....eee...eeeeee..eeeeee.eeeee...eeeeee.......hhhhhh.......eeee...........hhhhh....hhhhhhhhhhhhhhhhhh.....eee.........hhhhhhhhhhhhhhhh.....eeeeeeeee..eeeeeeeeee..eeeeeeeee....hhhhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tvw C   1 STLRLLISDSYDPWFNLAVAECIFRQMPATQRVLFLWRNADTVVIGRAQNPWKECNTRRMEEDNVRLARRSSGGGAVFHDLGNTCFTFMAGKPEYDKTISTSIVLNALNALGVSAEASGRNDLVVKTVEGDRKVSGSAYRETKDRGAHGGTLLLNADLSRLANYLNPDKKKLAAKGITSVRSRVTNLTELLPGITHEQVCEAITEAFFAHYGERVEAEIISPNKTPDLPNFAETFARQSSWEWNFGQAPAFSHLLDERFTWGGVELHFDVEKGHITRAQVFTDSLNPAPLEALAGRLQGCLYRADMLQQECEALLVDFPEQEKELRELSAWMAGAVR 337
                                    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       


Chain D from PDB  Type:PROTEIN  Length:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhh....eeeeeee...eeee....hhhhhhhhhhhhhh..eeee.......eee....eeeeeeee....hhhhhhhhhhhhhhh.....ee.....eeeee..eeeeee.eeeee...eeeeee......hhhhhhh.......eeee...........hhhhh....hhhhhhhhhhhhhhhhhh....eeee.........hhhhhhhhhhhhhhhh.....eeeeeeeee..eeeeeeeeee..eeeeeeeee....hhhhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tvw D   1 STLRLLISDSYDPWFNLAVAECIFRQMPATQRVLFLWRNADTVVIGRAQNPWKECNTRRMEEDNVRLARRSSGGGAVFHDLGNTCFTFMAGKPEYDKTISTSIVLNALNALGVSAEASGRNDLVVKTVEGDRKVSGSAYRETKDRGAHGGTLLLNADLSRLANYLNPDKKKLAAKGITSVRSRVTNLTELLPGITHEQVCEAITEAFFAHYGERVEAEIISPNKTPDLPNFAETFARQSSWEWNFGQAPAFSHLLDERFTWGGVELHFDVEKGHITRAQVFTDSLNPAPLEALAGRLQGCLYRADMLQQECEALLVDFPEQEKELRELSAWMAGAVR 337
                                    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
   Legend:   → Mismatch (orange background)
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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 4TVW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

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  4tvw
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  LPLA_ECOLI | P32099
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  2.7.7.63
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 Related Entries

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

UniProtKB/Swiss-Prot
        LPLA_ECOLI | P32099: 1x2g 1x2h 3a7a 3a7r 4tvy

(-) Related Entries Specified in the PDB File

3a7r 3A7R CONTAINS THE WT FORM OF THE PROTEIN IN THE SAME CONFORMATION
4tvy APO RESORUFIN LIGASE