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(-) Description

Title :  CRYSTAL STRUCTURES OF THE TRICORN INTERACTING FACOR F3 FROM THERMOPLASMA ACIDOPHILUM, A ZINC AMINOPEPTIDASE IN THREE DIFFERENT CONFORMATIONS
 
Authors :  O. J. P. Kyrieleis, P. Goettig, R. Kiefersauer, R. Huber, H. Brandstetter
Date :  07 Mar 05  (Deposition) - 31 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Zinc Aminopeptidase, Gluzincins, Superhelix, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. J. P. Kyrieleis, P. Goettig, R. Kiefersauer, R. Huber, H. Brandstetter
Crystal Structures Of The Tricorn Interacting Factor F3 From Thermoplasma Acidophilum, A Zinc Aminopeptidase In Three Different Conformations
J. Mol. Biol. V. 394 787 2005
PubMed-ID: 15893768  |  Reference-DOI: 10.1016/J.JMB.2005.03.070
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRICORN PROTEASE INTERACTING FACTOR F3
    Chains: A
    EC Number: 3.4.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSET6C
    Expression System Strain: BL21(DE3)RILL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 2303

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:265 , GLU A:266 , HIS A:269 , GLU A:288BINDING SITE FOR RESIDUE ZN A 800
2AC2SOFTWARETYR A:194 , LYS A:256 , ARG A:257BINDING SITE FOR RESIDUE SO4 A 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z1W)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His A:738 -Pro A:739

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z1W)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.TRF3_THEAC262-271  1A:262-271

(-) Exons   (0, 0)

(no "Exon" information available for 1Z1W)

(-) 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:780
 aligned with TRF3_THEAC | O93655 from UniProtKB/Swiss-Prot  Length:780

    Alignment length:780
                                    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       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780
           TRF3_THEAC     1 MEVEKYDLTLDFDIQKRTFNGTETITADAGDIVLDAVGLQINWMKVNGRDTAFTYDGQTVRAPGDSQPQKIEISFAGKVSDSLSGIYYAGRENGMITTHFEATDARRMFPCVDHPAYKAVFAITVVIDKDYDAISNMPPKRIEVSERKVVEFQDTPRMSTYLLYVGIGKFRYEYEKYRDIDLILASLKDIRSKYPLDMARKSVEFYENYFGIPYALPKMHLISVPEFGAGAMENWGAITFREIYMDIAENSAVTVKRNSANVIAHEIAHQWFGDLVTMKWWNDLWLNESFATFMSYKTMDTLFPEWSFWGDFFVSRTSGALRSDSLKNTHPIEVDVRDPDEISQIFDEISYGKGASILRMIEDYAGYEEFRKGISKYLNDHKFGNAEGSDLWTAIEDVSGKPVKRVMEYWIKNPGYPVIKLKRNGRKITMYQTRFLLNGEEEGRWPVPVNIKKKDGVERILLEDEASIEADGLIKINADSAGFYRVLYDDATFSDVMGHYRDLSPLDRIGLVDDLFAFLLSGHIDPETYRQRIRNFFDDEDHNVITAIVGQMEYLRMLTHAFDDDARAFCRSRMQFLTGKQDENLKIALGRVSRLYVMVDESYAEEMSKLFKDFDSAEPEMRSSIATAYALVTGDLKGLLEKFRSVDRDEDRVRIISAFGKLKSNTDLSTVYGMVEKTEIKKQDMISFFSSALETLPGREFIFANLDRIIRLVIRYFTGNRTASRTVEMMIPVIGLDHPDAEDIVRNIGSKNISMGLAKGIEMLAVNRKLVERIRQTAVK 780
               SCOP domains d1z1wa1 A:1-170 Tricorn protease interacting factor F3 N-terminal domain                                                                                                  d1z1wa2 A:171-414 Tricorn protease interacting factor F3 catalytic domain                                                                                                                                                                           d1z1wa3 A:415-489 Tricorn protease interacting factor F3 insert domain     d1z1wa4 A:490-780 Tricorn protease interacting factor F3 C-terminal domain                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains Peptidase_M1-1z1wA01 A:1-354                                                                                                                                                                                                                                                                                                                                      ----------------------------------------------------------------------------------------------------------------------DUF3358-1z1wA02 A:473-744                                                                                                                                                                                                                                                       ------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeee....eeeeeeeeee..eeeeee....eeeeeee...ee..ee...eeeeeee....eeeeeeeee......eeeee.....eeeee....hhhhh...........eeeeeeee....eeee...eeeeee...eeeee......hhhhh.eeee..eeeeeee..eeeeeee......hhhhhhhhhhhhhhhhhhh......eeeeeee......ee....eeeeehhhhh.....hhhhhhhhhhhhhhhhhhh.....ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhh.hhhhhhhhhhhh...eeeeeee...eeeeeeeee....eee....eeeeee....eeeeee...eeee.....ee.hhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhh..................hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1z1w A   1 MEVEKYDLTLDFDIQKRTFNGTETITADAGDIVLDAVGLQINWMKVNGRDTAFTYDGQTVRAPGDSQPQKIEISFAGKVSDSLSGIYYAGRENGMITTHFEATDARRMFPCVDHPAYKAVFAITVVIDKDYDAISNMPPKRIEVSERKVVEFQDTPRMSTYLLYVGIGKFRYEYEKYRDIDLILASLKDIRSKYPLDMARKSVEFYENYFGIPYALPKMHLISVPEFGAGAMENWGAITFREIYMDIAENSAVTVKRNSANVIAHEIAHQWFGDLVTMKWWNDLWLNESFATFMSYKTMDTLFPEWSFWGDFFVSRTSGALRSDSLKNTHPIEVDVRDPDEISQIFDEISYGKGASILRMIEDYAGYEEFRKGISKYLNDHKFGNAEGSDLWTAIEDVSGKPVKRVMEYWIKNPGYPVIKLKRNGRKITMYQTRFLLNGEEEGRWPVPVNIKKKDGVERILLEDEASIEADGLIKINADSAGFYRVLYDDATFSDVMGHYRDLSPLDRIGLVDDLFAFLLSGHIDPETYRQRIRNFFDDEDHNVITAIVGQMEYLRMLTHAFDDDARAFCRSRMQFLTGKQDENLKIALGRVSRLYVMVDESYAEEMSKLFKDFDSAEPEMRSSIATAYALVTGDLKGLLEKFRSVDRDEDRVRIISAFGKLKSNTDLSTVYGMVEKTEIKKQDMISFFSSALETLPGREFIFANLDRIIRLVIRYFTGNRTASRTVEMMIPVIGLDHPDAEDIVRNIGSKNISMGLAKGIEMLAVNRKLVERIRQTAVK 780
                                    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       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780
   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  (4, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Z1W)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_MA (251)
(-)
Clan: no clan defined [family: DUF3358] (5)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TRF3_THEAC | O93655)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    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: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: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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TRF3_THEAC | O93655: 1z5h 3q7j

(-) Related Entries Specified in the PDB File

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