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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PH0078 PROTEIN FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  H. Mizutani, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  09 Jun 06  (Deposition) - 09 Dec 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Mizutani, N. Kunishima
Crystal Structure Of The Ph0078 Protein From Pyrococcus Horikoshii Ot3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 361AA LONG HYPOTHETICAL D-AMINOPEPTIDASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PH0078
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: PH0078 PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:251 , ARG A:253 , HOH A:1056 , GLY B:252BINDING SITE FOR RESIDUE CL A 1001
2AC2SOFTWAREGLY A:252 , THR B:251 , ARG B:253BINDING SITE FOR RESIDUE CL B 1002
3AC3SOFTWARETHR C:251 , ARG C:253 , GLY D:252BINDING SITE FOR RESIDUE CL C 1003
4AC4SOFTWAREGLY C:252 , THR D:251 , ARG D:253BINDING SITE FOR RESIDUE CL D 1004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:46 -Pro A:47
2Gly B:46 -Pro B:47
3Gly C:46 -Pro C:47
4Gly D:46 -Pro D:47

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DRH)

(-) 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:354
 aligned with O57784_PYRHO | O57784 from UniProtKB/TrEMBL  Length:361

    Alignment length:359
                                    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         
         O57784_PYRHO     1 MKAQELGIKIGVFKPGKRNKITDVKGVKVGHVTLIKGKGKLIPGKGPVRTGVTAILPHEGNIYKEKVLAGAFVMNGYSKPVGLIQLWELGTIETPIILTNTLSIGTAVEGLLDYILEENEDIGVTTGSVNPLVLECNDSYLNDIRGRHVKREHVVEAIKRADEDFEEGAVGAGTGMSAFEFKGGIGSASRIVEIEGKKYTVGALVLSNFGRREDLTIAGVPVGLELKNWPGRGGEGKGSIIMIIATDAPLTGRQLNRVAKRAIVGLARTGGYAYNGSGDIAVAFSTANRIKHYEKEVIEIKALPDSVISPLFKATAEAVEEAIINSLLEARTMDGRDNHVRYALPKEELLRIMRRYGRL 359
               SCOP domains d2drha_ A: automated matches                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2drhA00 A:1-359 L-amino peptidase D-ALA esterase/amidase                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh............hhhhh...eeeeeeeee...........eeeeeeeee........eeeeeeeeeeee.....hhhhhhhhhee...eeeee..hhhhhhhhhhhhhhhhh............eeeee......hhhhh..hhhhhhhhhhhh........hhhhh..ee..ee.eeeeeeeeee....eeeeeeeeee...hhhhh.....hhhhhh.......-----.eeeeeee....hhhhhhhhhhhhhhhhhhh........eeeeeeeeeeeeee......eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhh.ee...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2drh A   1 MKAQELGIKIGVFKPGKRNKITDVKGVKVGHVTLIKGKGKLIPGKGPVRTGVTAILPHEGNIYKEKVLAGAFVMNGYSKPVGLIQLWELGTIETPIILTNTLSIGTAVEGLLDYILEENEDIGVTTGSVNPLVLECNDSYLNDIRGRHVKREHVVEAIKRADEDFEEGAVGAGTGMSAFEFKGGIGSASRIVEIEGKKYTVGALVLSNFGRREDLTIAGVPVGLELKNWPGRG-----SIIMIIATDAPLTGRQLNRVAKRAIVGLARTGGYAYNGSGDIAVAFSTANRIKHYEKEVIEIKALPDSVISPLFKATAEAVEEAIINSLLEARTMDGRDNHVRYALPKEELLRIMRRYGRL 359
                                    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         
                                                                                                                                                                                                                                                                  233   239                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:353
 aligned with O57784_PYRHO | O57784 from UniProtKB/TrEMBL  Length:361

    Alignment length:359
                                    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         
         O57784_PYRHO     1 MKAQELGIKIGVFKPGKRNKITDVKGVKVGHVTLIKGKGKLIPGKGPVRTGVTAILPHEGNIYKEKVLAGAFVMNGYSKPVGLIQLWELGTIETPIILTNTLSIGTAVEGLLDYILEENEDIGVTTGSVNPLVLECNDSYLNDIRGRHVKREHVVEAIKRADEDFEEGAVGAGTGMSAFEFKGGIGSASRIVEIEGKKYTVGALVLSNFGRREDLTIAGVPVGLELKNWPGRGGEGKGSIIMIIATDAPLTGRQLNRVAKRAIVGLARTGGYAYNGSGDIAVAFSTANRIKHYEKEVIEIKALPDSVISPLFKATAEAVEEAIINSLLEARTMDGRDNHVRYALPKEELLRIMRRYGRL 359
               SCOP domains d2drhb_ B: automated matches                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2drhB00 B:1-359 L-amino peptidase D-ALA esterase/amidase                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh............hhhhh...eeeeeeeee...........eeeeeeeee........eeeeeeeeeee......hhhhhhhhhee...eeeee..hhhhhhhhhhhhhhhhh............eeeee......hhhhh..hhhhhhhhhhhh........hhhhh..ee..ee.eeeeeeeeeee..eeeeeeeeeee...hhhhh.....hhhhhh......------.eeeeeee....hhhhhhhhhhhhhhhhhhh.........eeeeeeeeeeeee......eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh.ee...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2drh B   1 MKAQELGIKIGVFKPGKRNKITDVKGVKVGHVTLIKGKGKLIPGKGPVRTGVTAILPHEGNIYKEKVLAGAFVMNGYSKPVGLIQLWELGTIETPIILTNTLSIGTAVEGLLDYILEENEDIGVTTGSVNPLVLECNDSYLNDIRGRHVKREHVVEAIKRADEDFEEGAVGAGTGMSAFEFKGGIGSASRIVEIEGKKYTVGALVLSNFGRREDLTIAGVPVGLELKNWPGR------SIIMIIATDAPLTGRQLNRVAKRAIVGLARTGGYAYNGSGDIAVAFSTANRIKHYEKEVIEIKALPDSVISPLFKATAEAVEEAIINSLLEARTMDGRDNHVRYALPKEELLRIMRRYGRL 359
                                    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         
                                                                                                                                                                                                                                                                 232    239                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:353
 aligned with O57784_PYRHO | O57784 from UniProtKB/TrEMBL  Length:361

    Alignment length:359
                                    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         
         O57784_PYRHO     1 MKAQELGIKIGVFKPGKRNKITDVKGVKVGHVTLIKGKGKLIPGKGPVRTGVTAILPHEGNIYKEKVLAGAFVMNGYSKPVGLIQLWELGTIETPIILTNTLSIGTAVEGLLDYILEENEDIGVTTGSVNPLVLECNDSYLNDIRGRHVKREHVVEAIKRADEDFEEGAVGAGTGMSAFEFKGGIGSASRIVEIEGKKYTVGALVLSNFGRREDLTIAGVPVGLELKNWPGRGGEGKGSIIMIIATDAPLTGRQLNRVAKRAIVGLARTGGYAYNGSGDIAVAFSTANRIKHYEKEVIEIKALPDSVISPLFKATAEAVEEAIINSLLEARTMDGRDNHVRYALPKEELLRIMRRYGRL 359
               SCOP domains d2drhc_ C: automated matches                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2drhC00 C:1-359 L-amino peptidase D-ALA esterase/amidase                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh............hhhhh...eeeeeeeee...........eeeeeeeee........eeeeeeeeeee......hhhhhhhhhee...eeeee..hhhhhhhhhhhhhhhhh............eeeee......hhhhh..hhhhhhhhhhhh........hhhhh..ee..ee.eeeeeeeeeee..eeeeeeeeeee...hhhhh.....hhhhhh......------.eeeeeee....hhhhhhhhhhhhhhhhhhh.........eeeeeeeeeeeee......eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhh.ee...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2drh C   1 MKAQELGIKIGVFKPGKRNKITDVKGVKVGHVTLIKGKGKLIPGKGPVRTGVTAILPHEGNIYKEKVLAGAFVMNGYSKPVGLIQLWELGTIETPIILTNTLSIGTAVEGLLDYILEENEDIGVTTGSVNPLVLECNDSYLNDIRGRHVKREHVVEAIKRADEDFEEGAVGAGTGMSAFEFKGGIGSASRIVEIEGKKYTVGALVLSNFGRREDLTIAGVPVGLELKNWPGR------SIIMIIATDAPLTGRQLNRVAKRAIVGLARTGGYAYNGSGDIAVAFSTANRIKHYEKEVIEIKALPDSVISPLFKATAEAVEEAIINSLLEARTMDGRDNHVRYALPKEELLRIMRRYGRL 359
                                    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         
                                                                                                                                                                                                                                                                 232    239                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:353
 aligned with O57784_PYRHO | O57784 from UniProtKB/TrEMBL  Length:361

    Alignment length:358
                                    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        
         O57784_PYRHO     1 MKAQELGIKIGVFKPGKRNKITDVKGVKVGHVTLIKGKGKLIPGKGPVRTGVTAILPHEGNIYKEKVLAGAFVMNGYSKPVGLIQLWELGTIETPIILTNTLSIGTAVEGLLDYILEENEDIGVTTGSVNPLVLECNDSYLNDIRGRHVKREHVVEAIKRADEDFEEGAVGAGTGMSAFEFKGGIGSASRIVEIEGKKYTVGALVLSNFGRREDLTIAGVPVGLELKNWPGRGGEGKGSIIMIIATDAPLTGRQLNRVAKRAIVGLARTGGYAYNGSGDIAVAFSTANRIKHYEKEVIEIKALPDSVISPLFKATAEAVEEAIINSLLEARTMDGRDNHVRYALPKEELLRIMRRYGR 358
               SCOP domains d2drhd_ D: automated matches                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2drhD00 D:1-358 L-amino peptidase D-ALA esterase/amidase                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh............hhhhh...eeeeeeeee...........eeeeeeeee........eeeeeeeeeeee.....hhhhhhhhhee...eeeee..hhhhhhhhhhhhhhhhh............eeeee......hhhhh..hhhhhhhhhhhh........hhhhh..ee..ee.eeeeeeeeee....eeeeeeeeee...hhhhh.....hhhhhh.......-----.eeeeeee....hhhhhhhhhhhhhhhhhhh........eeeeeeeeeeeeee......eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhh.ee...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2drh D   1 MKAQELGIKIGVFKPGKRNKITDVKGVKVGHVTLIKGKGKLIPGKGPVRTGVTAILPHEGNIYKEKVLAGAFVMNGYSKPVGLIQLWELGTIETPIILTNTLSIGTAVEGLLDYILEENEDIGVTTGSVNPLVLECNDSYLNDIRGRHVKREHVVEAIKRADEDFEEGAVGAGTGMSAFEFKGGIGSASRIVEIEGKKYTVGALVLSNFGRREDLTIAGVPVGLELKNWPGRG-----SIIMIIATDAPLTGRQLNRVAKRAIVGLARTGGYAYNGSGDIAVAFSTANRIKHYEKEVIEIKALPDSVISPLFKATAEAVEEAIINSLLEARTMDGRDNHVRYALPKEELLRIMRRYGR 358
                                    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        
                                                                                                                                                                                                                                                                  233   239
   Legend:   → Mismatch (orange background)
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  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, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (O57784_PYRHO | O57784)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
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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