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(-) Description

Title :  STRUCTURE OF PEROXISOMAL TARGETING SIGNAL 1 (PTS1) BINDING DOMAIN OF TRYPANOSOMA BRUCEI PEROXIN 5 (TBPEX5)COMPLEXED TO T. BRUCEI GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (GAPDH) PTS1 PEPTIDE
 
Authors :  P. Sampathkumar, C. Roach, P. A. M Michels, W. G. J. Hol
Date :  18 Apr 08  (Deposition) - 24 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tpr Motifs, Tpr Protein, Peroxin 5, Pex5, Pts1 Binding Domain, Protein-Peptide Complex, Receptor, Tpr Repeat, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Sampathkumar, C. Roach, P. A. Michels, W. G. Hol
Structural Insights Into The Recognition Of Peroxisomal Targeting Signal 1 By Trypanosoma Brucei Peroxin 5.
J. Mol. Biol. V. 381 867 2008
PubMed-ID: 18598704  |  Reference-DOI: 10.1016/J.JMB.2008.05.089
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEROXISOME TARGETING SIGNAL 1 RECEPTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSKB3
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Fragment: BINDING DOMAIN,UNP RESIDUES 332-655
    Gene: PEX5
    Mutation: YES
    Organism Scientific: TRYPANOSOMA BRUCEI
 
Molecule 2 - T. BRUCEI GAPDH PTS1 PEPTIDE AC-DRDAAKL
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 22)

Asymmetric/Biological Unit (1, 22)
No.NameCountTypeFull Name
1EDO22Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:344 , PRO A:345 , TYR A:346 , LEU A:370 , GLU A:373 , ALA A:374BINDING SITE FOR RESIDUE EDO A 1
02AC2SOFTWAREASP A:618 , MET A:622 , ARG B:3BINDING SITE FOR RESIDUE EDO A 2
03AC3SOFTWAREGLU A:381 , GLU A:383 , GLU A:384BINDING SITE FOR RESIDUE EDO A 3
04AC4SOFTWAREALA A:394 , ASN A:538 , TYR A:567 , ARG A:569 , LEU B:7BINDING SITE FOR RESIDUE EDO B 8
05AC5SOFTWAREGLN A:535 , LYS A:539BINDING SITE FOR RESIDUE EDO A 5
06AC6SOFTWAREGLN A:501 , LYS A:539BINDING SITE FOR RESIDUE EDO A 6
07AC7SOFTWAREALA A:421 , ALA A:424 , LEU A:440 , TRP A:443 , SER A:505BINDING SITE FOR RESIDUE EDO A 7
08AC8SOFTWAREGLN A:501 , ASP A:533 , GLN A:535 , LEU A:536 , LYS A:539BINDING SITE FOR RESIDUE EDO A 8
09AC9SOFTWAREALA A:421 , TRP A:443BINDING SITE FOR RESIDUE EDO A 9
10BC1SOFTWAREASN A:407 , HIS A:427BINDING SITE FOR RESIDUE EDO A 10
11BC2SOFTWAREGLU A:611 , ALA A:612 , ARG A:614 , SER A:615BINDING SITE FOR RESIDUE EDO A 11
12BC3SOFTWARELEU A:437 , ARG A:441 , GLU A:481 , GLU A:484 , CYS A:485BINDING SITE FOR RESIDUE EDO A 12
13BC4SOFTWAREASN A:511 , LEU A:512 , ASN A:514 , TYR A:516 , LEU A:655BINDING SITE FOR RESIDUE EDO A 13
14BC5SOFTWAREPRO A:531BINDING SITE FOR RESIDUE EDO A 14
15BC6SOFTWAREARG A:524 , GLU A:552 , ALA A:556BINDING SITE FOR RESIDUE EDO A 15
16BC7SOFTWARELEU A:360 , ALA A:363 , ASN A:364 , LEU A:365 , ASN A:480 , ASN A:564 , GLY A:566BINDING SITE FOR RESIDUE EDO A 16
17BC8SOFTWAREPRO A:448 , GLU A:451BINDING SITE FOR RESIDUE EDO A 17
18BC9SOFTWAREASN A:546 , ASN A:548BINDING SITE FOR RESIDUE EDO A 18
19CC1SOFTWARELYS A:398 , ASP A:399 , GLY A:400 , LEU A:401BINDING SITE FOR RESIDUE EDO A 19
20CC2SOFTWAREGLU A:397 , ASP A:399 , ARG A:569BINDING SITE FOR RESIDUE EDO A 20
21CC3SOFTWAREPRO A:414 , SER A:446BINDING SITE FOR RESIDUE EDO A 21
22CC4SOFTWAREARG A:410 , HIS A:420 , LEU A:423 , SER A:439BINDING SITE FOR RESIDUE EDO A 22

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CVN)

(-) 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:300
 aligned with Q57W55_TRYB2 | Q57W55 from UniProtKB/TrEMBL  Length:655

    Alignment length:320
                                   345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655
         Q57W55_TRYB2   336 TDYPFEANNPYMYHENPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNVEPFAKEFGLQSMLL 655
               SCOP domains d3cvna_ A: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhh..---------------....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.-----.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cvn A 336 TDYPFEANNPYMYHENPMEEGLSMLKLANLAEAALAFEAVCQAAPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQLGSVNL---------------FFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVG-----GEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNVEPFAKEFGLQSMLL 655
                                   345       355       365       375       385       395       405       415       425       435       445       455  |      -       475       485       495       505       515       525       535       545       555       565       575       585       595    |    -|      615       625       635       645       655
                                                                                                                                                    458             474                                                                                                                           600   606                                                 


Chain A from PDB  Type:PROTEIN  Length:300
 aligned with Q9U7C3_9TRYP | Q9U7C3 from UniProtKB/TrEMBL  Length:655

    Alignment length:320
                                   345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655
         Q9U7C3_9TRYP   336 TDYPFEANNPYMYHENPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNVEPFAKEFGLQSMLL 655
               SCOP domains d3cvna_ A: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhh..---------------....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.-----.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cvn A 336 TDYPFEANNPYMYHENPMEEGLSMLKLANLAEAALAFEAVCQAAPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQLGSVNL---------------FFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVG-----GEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNVEPFAKEFGLQSMLL 655
                                   345       355       365       375       385       395       405       415       425       435       445       455  |      -       475       485       495       505       515       525       535       545       555       565       575       585       595    |    -|      615       625       635       645       655
                                                                                                                                                    458             474                                                                                                                           600   606                                                 


Chain B from PDB  Type:PROTEIN  Length:5
 aligned with G3PG_TRYBB | P22512 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:5
           G3PG_TRYBB   355 RAAKL 359
               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
                 3cvn B   3 RAAKL   7
   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, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q57W55_TRYB2 | Q57W55)
molecular function
    GO:0005052    peroxisome matrix targeting signal-1 binding    Interacting selectively and non-covalently with a type 1 peroxisome targeting signal, a tripeptide with the consensus sequence (S/A/C)-(K/R/H)-L.
    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).
biological process
    GO:0016560    protein import into peroxisome matrix, docking    The process in which a complex formed of a peroxisome targeting sequence (PTS) receptor bound to a PTS-bearing protein docks with translocation machinery in the peroxisomal membrane.
cellular component
    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:0005778    peroxisomal membrane    The lipid bilayer surrounding a peroxisome.

Chain A   (Q9U7C3_9TRYP | Q9U7C3)

Chain B   (G3PG_TRYBB | P22512)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0004365    glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity    Catalysis of the reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH + H+.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016620    oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
biological process
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0020015    glycosome    A membrane-bounded organelle found in organisms from the order Kinetoplastida that houses the enzymes of glycolysis.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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  3cvn
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 Related Entries

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

UniProtKB/Swiss-Prot
        G3PG_TRYBB | P22512: 2x0n
        Q9U7C3_9TRYP | Q9U7C3: 3cv0 3cvp 3cvq
UniProtKB/TrEMBL
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(-) Related Entries Specified in the PDB File

3cv0 SAME PROTEIN COMPLEXED WITH T.BRUCEI PHOSPHOGLUCO ISOMERASE (TBPGI) PTS1 PEPTIDE
3cvl SAME PROTEIN COMPLEXED WITH T.BRUCEI PHOSPHOFRUCTO KINASE (TBPFK) PTS1 PEPTIDE
3cvp SAME PROTEIN COMPLEX WITH PTS1 PEPTIDE (10-SKL WITH THE SEQUENCE ACGTLSNRASKL)
3cvq SAME PROTEIN COMPLEX WITH PTS1 PEPTIDE (7-SKL WITH THE SEQUENCE SNRWSKL)