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(-) Description

Title :  ENGINEERED THERMOPLASMA ACIDOPHILUM F3 FACTOR MIMICS HUMAN AMINOPEPTIDASE N (APN) AS A TARGET FOR ANTICANCER DRUG DEVELOPMENT
 
Authors :  J. Su, Q. Wang, J. Feng, C. Zhang, D. Zhu, T. We, W. Xu, L. Gu
Date :  05 Jan 11  (Deposition) - 27 Jul 11  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.91
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Trf3, Inhibitor Fbo, Aminopeptidase, Inhibitor Binding, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Su, Q. Wang, J. Feng, C. Zhang, D. Zhu, T. Wei, W. Xu, L. Gu
Engineered Thermoplasma Acidophilum Factor F3 Mimics Human Aminopeptidase N (Apn) As A Target For Anticancer Drug Development
Bioorg. Med. Chem. V. 19 2991 2011
PubMed-ID: 21493078  |  Reference-DOI: 10.1016/J.BMC.2011.03.028

(-) Compounds

Molecule 1 - TRICORN PROTEASE-INTERACTING FACTOR F3
    Chains: A, B
    EC Number: 3.4.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: O93655, TA0815, TRF3
    Mutation: YES
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 273075
    Strain: DSM 1728

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1FBO1Ligand/IonL-PHENYLALANYL-N6-[(BENZYLOXY)CARBONYL]-N1-HYDROXY-L-LYSINAMIDE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FBO1Ligand/IonL-PHENYLALANYL-N6-[(BENZYLOXY)CARBONYL]-N1-HYDROXY-L-LYSINAMIDE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1FBO-1Ligand/IonL-PHENYLALANYL-N6-[(BENZYLOXY)CARBONYL]-N1-HYDROXY-L-LYSINAMIDE
2ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:265 , GLU A:266 , HIS A:269 , GLU A:288 , FBO A:900BINDING SITE FOR RESIDUE ZN A 800
2AC2SOFTWAREHIS A:99 , GLN A:101 , ALA A:229 , GLY A:230 , ALA A:231 , GLU A:233 , TYR A:244 , HIS A:265 , GLU A:266 , GLU A:288 , THR A:292 , ARG A:316 , GLU A:348 , TYR A:351 , GLY A:352 , ZN A:800BINDING SITE FOR RESIDUE FBO A 900
3AC3SOFTWAREGLU B:233 , HIS B:265 , HIS B:269 , GLU B:288BINDING SITE FOR RESIDUE ZN B 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q7J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q7J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q7J)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.TRF3_THEAC262-271
 		  2A:262-271
B:262-271
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.TRF3_THEAC262-271
 		  1A:262-271
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.TRF3_THEAC262-271
 		  1-
B:262-271

(-) Exons   (0, 0)

(no "Exon" information available for 3Q7J)

(-) 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: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 d3q7ja1 A:1-170 automated matches                                                                                                                                         d3q7ja2 A:171-414 automated matches                                                                                                                                                                                                                 d3q7ja3 A:415-489 automated matches                                        d3q7ja4 A:490-780 automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeee....eeeeeeeeee....eeee.......eeee.......ee...eeee......eeeeeeeeee......eeeee.....eeeee....hhhhh..........eeeeeeeee....eeee...eeeeee...eeeee....eehhhhh.eeee..eeeeeee..eeeeeee......hhhhhhhhhhhhhhhhhhh......eeeeeee......ee....eeeee.hhh........hhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeehhhhhhhhhhhhhh.hhhhhhhhhhhh...eeeeeeee..eeeeeeeee....eee....eeeeeee...eeeeee...eeee...eeee.hhhh...eee.hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3q7j A   1 MEVEKYDLTLDFDIQKRTFNGTETITADAGDIVLDAVGLQINWMKVNGRDTAFTYDGQTVRAPGDSQPQKIEISFAGKVSDSLSGIYYAGRENGMITTHFQATDARRMFPCVDHPAYKAVFAITVVIDKDYDAISNMPPKRIEVSERKVVEFQDTPRMSTYLLYVGIGKFRYEYEKYRDIDLILASLKDIRSKYPLDMARKSVEFYENYFGIPYALPKMHLISVPEFGAGAMENWGAITFREIYMDIAENSAVTVKRNSATVIAHEIAHQWFGDLVTMKWWNDLWLNESFATFMSYKTMDTLFPEWSFWGDFFVSRTSGALRSDSLKNTHPIEVDVRDPDEISQIFDEISYGKGASILRMIEDYAGYEEFRKGISKYLNDHKFGNAEGSDLWTAIEDVSGKPVKRVMEYWIKNPGYPVIKLKRNGRKITMYQTRFLLNGEEEGRWPVPVNIKKKDGVERILLEDEASIEADGLIKINADSAGFYRVLYDDATFSDVMGHYRDLSPLDRIGLVDDLFAFLLSGHIDPETYRQRIRNFFDDEDHNVITAIVGQMEYLRMLTHAFDDDARAFCRSRMQFLTGKQDENLKIALGRVSRLYVMVDESYAEEMSKLFKDFDSAEPEMRSSIATAYALVTGDLKGLLEKFRSVDRDEDRVRIISAFGKLKSNTDLSTVYGMVEKTEIKKQDMISFFSSALETLPGREFIFANLDRIIRLVIRYFTGNRTASRTVEMMIPVIGLDHPDAEDIVRNIGSKNISMGLAKGIEMLAVNRKLVERIRQTAVK 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


Chain B 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 d3q7jb1 B:1-170 automated matches                                                                                                                                         d3q7jb2 B:171-414 automated matches                                                                                                                                                                                                                 d3q7jb3 B:415-489 automated matches                                        d3q7jb4 B:490-780 automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeee....eeeeeeeeee....eeee....eeeeeee..ee...ee...eeee......eeeeeeeeee......eeeee.....eeeee....hhhhh...........eeeeeeeee...eeee...eeeeee..eeeeee......hhhhh.eeee..eeeeeee..eeeeeee......hhhhhhhhhhhhhhhhhhh......eeeeeee......ee....eeeeehhhhh.....hhhhhhhhhhhhhhhhhh......eee.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhhhh.hhhhhhhhhhhh...eeee......eeeeeeeeee..eeee....eeeeeee...eeeeee...eeee...eeee.hhhh...eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhh....hhhhhhhh..........hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3q7j B   1 MEVEKYDLTLDFDIQKRTFNGTETITADAGDIVLDAVGLQINWMKVNGRDTAFTYDGQTVRAPGDSQPQKIEISFAGKVSDSLSGIYYAGRENGMITTHFQATDARRMFPCVDHPAYKAVFAITVVIDKDYDAISNMPPKRIEVSERKVVEFQDTPRMSTYLLYVGIGKFRYEYEKYRDIDLILASLKDIRSKYPLDMARKSVEFYENYFGIPYALPKMHLISVPEFGAGAMENWGAITFREIYMDIAENSAVTVKRNSATVIAHEIAHQWFGDLVTMKWWNDLWLNESFATFMSYKTMDTLFPEWSFWGDFFVSRTSGALRSDSLKNTHPIEVDVRDPDEISQIFDEISYGKGASILRMIEDYAGYEEFRKGISKYLNDHKFGNAEGSDLWTAIEDVSGKPVKRVMEYWIKNPGYPVIKLKRNGRKITMYQTRFLLNGEEEGRWPVPVNIKKKDGVERILLEDEASIEADGLIKINADSAGFYRVLYDDATFSDVMGHYRDLSPLDRIGLVDDLFAFLLSGHIDPETYRQRIRNFFDDEDHNVITAIVGQMEYLRMLTHAFDDDARAFCRSRMQFLTGKQDENLKIALGRVSRLYVMVDESYAEEMSKLFKDFDSAEPEMRSSIATAYALVTGDLKGLLEKFRSVDRDEDRVRIISAFGKLKSNTDLSTVYGMVEKTEIKKQDMISFFSSALETLPGREFIFANLDRIIRLVIRYFTGNRTASRTVEMMIPVIGLDHPDAEDIVRNIGSKNISMGLAKGIEMLAVNRKLVERIRQTAVK 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)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (4, 8)

Asymmetric 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 3Q7J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3Q7J)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  3q7j
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  3.4.11.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRF3_THEAC | O93655: 1z1w 1z5h

(-) Related Entries Specified in the PDB File

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