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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FTSH PROTEASE DOMAIN
 
Authors :  R. Suno, H. Niwa, D. Tsuchiya, X. Zhang, M. Yoshida, K. Morikawa
Date :  28 Mar 06  (Deposition) - 27 Jun 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.79
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Metalloproteinase, Hexamer-Ring, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Suno, H. Niwa, D. Tsuchiya, X. Zhang, M. Yoshida, K. Morikawa
Structure Of The Whole Cytosolic Region Of Atp-Dependent Protease Ftsh
Mol. Cell V. 22 575 2006
PubMed-ID: 16762831  |  Reference-DOI: 10.1016/J.MOLCEL.2006.04.020
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CELL DIVISION PROTEIN FTSH HOMOLOG
    Chains: A, B
    EC Number: 3.4.24.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 403-634
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: ZINC PROTEASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1HG2Ligand/IonMERCURY (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1HG-1Ligand/IonMERCURY (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:418 , HIS A:422 , ASP A:496BINDING SITE FOR RESIDUE HG A 1001
2AC2SOFTWAREHIS B:418 , HIS B:422 , ASP B:496BINDING SITE FOR RESIDUE HG B 2001

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:588 -A:606
2B:588 -B:606

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DI4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DI4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DI4)

(-) Exons   (0, 0)

(no "Exon" information available for 2DI4)

(-) 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:176
 aligned with FTSH_AQUAE | O67077 from UniProtKB/Swiss-Prot  Length:634

    Alignment length:202
                                   415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605  
           FTSH_AQUAE   406 TISPKEKEKIAIHEAGHALMGLVSDDDDKVHKISIIPRGMALGVTQQLPIEDKHIYDKKDLYNKILVLLGGRAAEEVFFGKDGITTGAENDLQRATDLAYRMVSMWGMSDKVGPIAIRRVANPFLGGMTTAVDTSPDLLREIDEEVKRIITEQYEKAKAIVEEYKEPLKAVVKKLLEKETITCEEFVEVFKLYGIELKDKCK 607
               SCOP domains d2di4a1 A:406-607 Cell division prot                ein FtsH, C-terminal domain                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh........ee..----------------....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............----------.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2di4 A 406 TISPKEKEKIAIHEAGHALMGLVSDDDDKVHKISII----------------KHIYDKKDLYNKILVLLGGRAAEEVFFGKDGITTGAENDLQRATDLAYRMVSMWGMSDKVGPIAIRR----------TAVDTSPDLLREIDEEVKRIITEQYEKAKAIVEEYKEPLKAVVKKLLEKETITCEEFVEVFKLYGIELKDKCK 607
                                   415       425       435     |   -         -  |    465       475       485       495       505       515        |-       535       545       555       565       575       585       595       605  
                                                             441              458                                                               524        535                                                                        


Chain B from PDB  Type:PROTEIN  Length:175
 aligned with FTSH_AQUAE | O67077 from UniProtKB/Swiss-Prot  Length:634

    Alignment length:201
                                   416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606 
           FTSH_AQUAE   407 ISPKEKEKIAIHEAGHALMGLVSDDDDKVHKISIIPRGMALGVTQQLPIEDKHIYDKKDLYNKILVLLGGRAAEEVFFGKDGITTGAENDLQRATDLAYRMVSMWGMSDKVGPIAIRRVANPFLGGMTTAVDTSPDLLREIDEEVKRIITEQYEKAKAIVEEYKEPLKAVVKKLLEKETITCEEFVEVFKLYGIELKDKCK 607
               SCOP domains d2di4b_ B: Cell division protein Fts                H, C-terminal domain                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh........ee...----------------...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..............----------.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2di4 B 407 ISPKEKEKIAIHEAGHALMGLVSDDDDKVHKISIIP----------------HIYDKKDLYNKILVLLGGRAAEEVFFGKDGITTGAENDLQRATDLAYRMVSMWGMSDKVGPIAIRR----------TAVDTSPDLLREIDEEVKRIITEQYEKAKAIVEEYKEPLKAVVKKLLEKETITCEEFVEVFKLYGIELKDKCK 607
                                   416       426       436     |   -         -  |    466       476       486       496       506       516       | -       536       546       556       566       576       586       596       606 
                                                             442              459                                                              524        535
   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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DI4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DI4)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FTSH_AQUAE | O67077)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004176    ATP-dependent peptidase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the hydrolysis of peptide bonds.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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)

UniProtKB/Swiss-Prot
        FTSH_AQUAE | O67077: 4ww0 4z8x

(-) Related Entries Specified in the PDB File

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