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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PROLINE IMINOPEPTIDASE-RELATED PROTEIN TTHA1809 FROM THERMUS THERMOPHILUS HB8
 
Authors :  M. Okai, Y. Miyauchi, A. Ebihara, W. C. Lee, K. Nagata, M. Tanokura
Date :  01 May 07  (Deposition) - 26 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ttha1809, Proline Iminopeptidase-Related Protein, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Okai, Y. Miyauchi, A. Ebihara, W. C. Lee, K. Nagata, M. Tanokura
Crystal Structure Of The Proline Iminopeptidase-Related Protein Ttha1809 From Thermus Thermophilus Hb8
Proteins V. 70 1646 2008
PubMed-ID: 18175319  |  Reference-DOI: 10.1002/PROT.21892

(-) Compounds

Molecule 1 - PROLINE IMINOPEPTIDASE-RELATED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 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  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:34 , TRP A:128 , HOH A:604 , HOH A:747 , HOH A:750BINDING SITE FOR RESIDUE GOL A 500
2AC2SOFTWAREPRO A:26 , ALA A:27 , GLY A:98 , GLU A:120 , HOH A:645BINDING SITE FOR RESIDUE GOL A 501
3AC3SOFTWAREGLU A:4 , ILE A:5 , GLY A:6 , HOH A:546 , HOH A:655 , HOH A:660BINDING SITE FOR RESIDUE GOL A 502
4AC4SOFTWAREGLY B:34 , TRP B:128 , HOH B:1556 , HOH B:1638 , HOH B:1640BINDING SITE FOR RESIDUE GOL B 1500
5AC5SOFTWAREARG A:137 , GLU A:140 , GLU B:44 , ALA B:180 , ILE B:259 , HOH B:1528 , HOH B:1530 , HOH B:1534 , HOH B:1576BINDING SITE FOR RESIDUE GOL B 1501
6AC6SOFTWAREALA A:145 , HOH A:692 , TYR B:40 , ARG B:43 , GLN B:47 , HOH B:1584BINDING SITE FOR RESIDUE GOL B 1502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YYS)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:34 -Pro A:35
2Tyr A:233 -Pro A:234
3Gly B:34 -Pro B:35
4Tyr B:233 -Pro B:234

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YYS)

(-) 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:284
 aligned with Q5SHC1_THET8 | Q5SHC1 from UniProtKB/TrEMBL  Length:286

    Alignment length:284
                                    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    
         Q5SHC1_THET8     1 MREEIGYVPVGEAELYVEDVGPVEGPALFVLHGGPGGNAYVLREGLQDYLEGFRVVYFDQRGSGRSLELPQDPRLFTVDALVEDTLLLAEALGVERFGLLAHGFGAVVALEVLRRFPQAEGAILLAPWVNFPWLAARLAEAAGLAPLPDPEENLKEALKREEPKALFDRLMFPTPRGRMAYEWLAEGAGILGSDAPGLAFLRNGLWRLDYTPYLTPERRPLYVLVGERDGTSYPYAEEVASRLRAPIRVLPEAGHYLWIDAPEAFEEAFKEALAALVPALRGPL 284
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeee......eeeee.......hhhhhhhhhhhh...eeeee.............hhhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhh......eeeeee........hhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhh.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yys A   1 MREEIGYVPVGEAELYVEDVGPVEGPALFVLHGGPGGNAYVLREGLQDYLEGFRVVYFDQRGSGRSLELPQDPRLFTVDALVEDTLLLAEALGVERFGLLAHGFGAVVALEVLRRFPQAEGAILLAPWVNFPWLAARLAEAAGLAPLPDPEENLKEALKREEPKALFDRLMFPTPRGRMAYEWLAEGAGILGSDAPGLAFLRNGLWRLDYTPYLTPERRPLYVLVGERDGTSYPYAEEVASRLRAPIRVLPEAGHYLWIDAPEAFEEAFKEALAALVPALRGPL 284
                                    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    


Chain B from PDB  Type:PROTEIN  Length:280
 aligned with Q5SHC1_THET8 | Q5SHC1 from UniProtKB/TrEMBL  Length:286

    Alignment length:280
                                    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
         Q5SHC1_THET8     1 MREEIGYVPVGEAELYVEDVGPVEGPALFVLHGGPGGNAYVLREGLQDYLEGFRVVYFDQRGSGRSLELPQDPRLFTVDALVEDTLLLAEALGVERFGLLAHGFGAVVALEVLRRFPQAEGAILLAPWVNFPWLAARLAEAAGLAPLPDPEENLKEALKREEPKALFDRLMFPTPRGRMAYEWLAEGAGILGSDAPGLAFLRNGLWRLDYTPYLTPERRPLYVLVGERDGTSYPYAEEVASRLRAPIRVLPEAGHYLWIDAPEAFEEAFKEALAALVPAL 280
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------Abhydrolase_6-2yysB01 B:28-268                                                                                                                                                                                                                   ------------ Pfam domains (1)
           Pfam domains (2) ---------------------------Abhydrolase_6-2yysB02 B:28-268                                                                                                                                                                                                                   ------------ Pfam domains (2)
         Sec.struct. author ..eeeeeeee..eeeeeeee......eeeee.......hhhhhhhhhhhh...eeeee..................hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhh......eeeeee.......hhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yys B   1 MREEIGYVPVGEAELYVEDVGPVEGPALFVLHGGPGGNAYVLREGLQDYLEGFRVVYFDQRGSGRSLELPQDPRLFTVDALVEDTLLLAEALGVERFGLLAHGFGAVVALEVLRRFPQAEGAILLAPWVNFPWLAARLAEAAGLAPLPDPEENLKEALKREEPKALFDRLMFPTPRGRMAYEWLAEGAGILGSDAPGLAFLRNGLWRLDYTPYLTPERRPLYVLVGERDGTSYPYAEEVASRLRAPIRVLPEAGHYLWIDAPEAFEEAFKEALAALVPAL 280
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 2YYS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: AB_hydrolase (347)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5SHC1_THET8 | Q5SHC1)
molecular function
    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.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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