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(-) Description

Title :  MUTANT N-TERMINAL DOMAIN OF MYCOBACTERIUM TUBERCULOSIS CLPC1, F2Y, BOUND TO CYCLOMARIN A
 
Authors :  D. Vasudevan, C. G. Noble
Date :  14 Jun 13  (Deposition) - 18 Sep 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.18
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chaperone, Chaperone-Antimicrobial Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Vasudevan, S. P. S. Rao, C. G. Noble
Structural Basis Of Mycobacterial Inhibition By Cyclomarin
J. Biol. Chem. V. 288 30883 2013
PubMed-ID: 24022489  |  Reference-DOI: 10.1074/JBC.M113.493767

(-) Compounds

Molecule 1 - PROBABLE ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 1-145
    Gene: CLPC
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: CLPC1
 
Molecule 2 - CYCLOMARIN A
    Chains: B
    Organism Scientific: STREPTOMYCES
    Organism Taxid: 1931

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 6)

Asymmetric/Biological Unit (6, 6)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MLE1Mod. Amino AcidN-METHYLLEUCINE
3WLU1Mod. Amino Acid(4R)-5-HYDROXY-N-METHYL-L-LEUCINE
4WPA1Mod. Amino Acid(BETAR)-BETA-METHOXY-L-PHENYLALANINE
5WRP1Mod. Amino Acid(BETAR)-BETA-HYDROXY-1-[(3R)-3-HYDROXY-2-METHYLBUTAN-2-YL]-L-TRYPTOPHAN
6WVL1Mod. Amino Acid(2S,3R)-2-AMINO-3,5-DIMETHYLHEX-4-ENOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:29 , THR A:30 , THR A:81 , GLN A:97 , LEU A:98 , GLY A:118 , VAL A:119BINDING SITE FOR RESIDUE ACT A 201
2AC2SOFTWAREMET A:1 , TYR A:2 , VAL A:14 , GLN A:17 , GLU A:18 , SER A:55 , GLU A:57 , HIS A:77 , PRO A:79 , PHE A:80 , LYS A:85 , GLU A:89 , GLN A:136 , HOH A:301 , HOH A:302 , HOH A:309 , HOH A:313 , HOH B:101 , HOH B:102 , HOH B:103 , HOH B:104 , HOH B:105 , HOH B:108BINDING SITE FOR CHAIN B OF CYCLOMARIN A

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WDD)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Wrp B:1 -Wlu B:2
2Val B:5 -Mle B:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WDD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WDD)

(-) Exons   (0, 0)

(no "Exon" information available for 3WDD)

(-) Sequences/Alignments

Asymmetric/Biological 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:147
 aligned with CLPC1_MYCTO | P9WPC8 from UniProtKB/Swiss-Prot  Length:848

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
          CLPC1_MYCTO     1 MFERFTDRARKVVVLAQEEARMLNHNYIGTEHILLGLIHEGEGVAAKSLESLGISLEGVRSQVEEIIGQGQQAPSGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVAAQVLVKLGAELTRVRQQVIQLLSGYQG 147
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wdd A   1 MYERFTDRARRVVVLAQEEARMLNHNYIGTEHILLGLIHEGEGVAAKSLESLGISLEGVRSQVEEIIGQGQQAPSGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVAAQVLVKLGAELTRVRQQVIQLLSGYLE 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       


Chain A from PDB  Type:PROTEIN  Length:147
 aligned with CLPC1_MYCTU | P9WPC9 from UniProtKB/Swiss-Prot  Length:848

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
          CLPC1_MYCTU     1 MFERFTDRARRVVVLAQEEARMLNHNYIGTEHILLGLIHEGEGVAAKSLESLGISLEGVRSQVEEIIGQGQQAPSGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVAAQVLVKLGAELTRVRQQVIQLLSGYQG 147
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wdd A   1 MYERFTDRARRVVVLAQEEARMLNHNYIGTEHILLGLIHEGEGVAAKSLESLGISLEGVRSQVEEIIGQGQQAPSGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVAAQVLVKLGAELTRVRQQVIQLLSGYLE 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       


Chain B from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 3wdd B   1 wlAfVlv   7
                            || | ||
                            1-WRP||
                             2-WLU|
                               4-WPA
                                 6-MLE
                                  7-WVL
   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  (0, 0)

(no "SCOP Domain" information available for 3WDD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WDD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WDD)

(-) Gene Ontology  (12, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CLPC1_MYCTO | P9WPC8)
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.
biological process
    GO:0019538    protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.

Chain A   (CLPC1_MYCTU | P9WPC9)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    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).
    GO:0044183    protein binding involved in protein folding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) that contributes to the process of protein folding.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0019538    protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

3wdb 3wdc 3wde