Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  HISTIDINOL PHOSPHATE PHOSPHATASE COMPLEXED WITH PHOSPHATE
 
Authors :  R. Omi
Date :  03 May 07  (Deposition) - 27 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Metal-Dependent, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Omi, M. Goto, I. Miyahara, M. Manzoku, A. Ebihara, K. Hirotsu
Crystal Structure Of Monofunctional Histidinol Phosphate Phosphatase From Thermus Thermophilus Hb8.
Biochemistry V. 46 12618 2007
PubMed-ID: 17929834  |  Reference-DOI: 10.1021/BI701204R

(-) Compounds

Molecule 1 - HISTIDINOL PHOSPHATASE
    Chains: A, B
    EC Number: 3.1.3.15
    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: 274
    Synonym: HISTIDINOL PHOSPHATE PHOSPHATASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1FE4Ligand/IonFE (III) ION
2GOL1Ligand/IonGLYCEROL
3PO42Ligand/IonPHOSPHATE ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2GOL2Ligand/IonGLYCEROL
3PO44Ligand/IonPHOSPHATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:13 , HIS A:38 , HIS A:226 , PO4 A:2001BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREGLU A:80 , HIS A:108 , HIS A:154 , FE A:503 , PO4 A:2001 , HOH A:2146BINDING SITE FOR RESIDUE FE A 502
3AC3SOFTWAREHIS A:5 , HIS A:7 , GLU A:80 , ASP A:224 , FE A:502 , PO4 A:2001 , HOH A:2146BINDING SITE FOR RESIDUE FE A 503
4AC4SOFTWAREHIS A:7 , HIS A:13 , HIS A:38 , HIS A:108 , ASP A:224 , HIS A:226 , ZN A:501 , FE A:502 , FE A:503 , HOH A:2118 , HOH A:2139BINDING SITE FOR RESIDUE PO4 A 2001
5AC5SOFTWAREGLU B:80 , HIS B:108 , HIS B:154 , FE B:1503 , PO4 B:2002 , HOH B:2151BINDING SITE FOR RESIDUE FE B 1502
6AC6SOFTWAREHIS B:13 , HIS B:38 , HIS B:226 , PO4 B:2002BINDING SITE FOR RESIDUE ZN B 1501
7AC7SOFTWAREHIS B:5 , HIS B:7 , GLU B:80 , ASP B:224 , FE B:1502 , PO4 B:2002 , HOH B:2151BINDING SITE FOR RESIDUE FE B 1503
8AC8SOFTWAREHIS B:7 , HIS B:13 , HIS B:38 , GLU B:80 , HIS B:108 , ASP B:224 , HIS B:226 , ZN B:1501 , FE B:1502 , FE B:1503 , HOH B:2090 , HOH B:2102 , HOH B:2151 , HOH B:2165BINDING SITE FOR RESIDUE PO4 B 2002
9AC9SOFTWARELEU A:10 , CYS A:11 , GLY A:12 , PRO A:47 , ARG A:50 , HOH A:2085BINDING SITE FOR RESIDUE GOL A 2003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YZ5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:203 -Pro A:204
2Tyr B:203 -Pro B:204

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YZ5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YZ5)

(-) Exons   (0, 0)

(no "Exon" information available for 2YZ5)

(-) 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:263
 aligned with Q5SLG2_THET8 | Q5SLG2 from UniProtKB/TrEMBL  Length:267

    Alignment length:263
                                    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   
         Q5SLG2_THET8     1 MVDSHVHTPLCGHAEGHPEAYLEEARAKGLKGVVFTDHSPMPPWYDPESRMRLEALPFYLLALERVRERAQDLYVGIGLEADFHPGTEGFLAQLLRRYPFDYVIGSVHYLGAWPLDHPDHQEEYAWRDLKEVFRAYFQEVEKAARSGLFHAIGHLDLPKKFGHRLPEEALLELAEPALRAVAEAGLFLDVNTAGLRRPAKEVYPAPALLRRARELGIGLVLGSDAHRPEEVGFAFPEVQALLAGLGFREAYYFVEGSPVAYPL 263
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhh....hhhhhhhhhhhh...eeee..........hhhhh.hhhhhhhhhhhhhhhhhhh...eeee.eeee....hhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee...hhhhh.....hhhhhhhhhhhhhhhhhhhh.eeeee.hhhh........hhhhhhhhhhh...eeee....hhhhh..hhhhhhhhhhhh...eeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yz5 A   1 MVDSHVHTPLCGHAEGHPEAYLEEARAKGLKGVVFTDHSPMPPWYDPESRMRLEALPFYLLALERVRERAQDLYVGIGLEADFHPGTEGFLAQLLRRYPFDYVIGSVHYLGAWPLDHPDHQEEYAWRDLKEVFRAYFQEVEKAARSGLFHAIGHLDLPKKFGHRLPEEALLELAEPALRAVAEAGLFLDVNTAGLRRPAKEVYPAPALLRRARELGIGLVLGSDAHRPEEVGFAFPEVQALLAGLGFREAYYFVEGSPVAYPL 263
                                    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   


Chain B from PDB  Type:PROTEIN  Length:265
 aligned with Q5SLG2_THET8 | Q5SLG2 from UniProtKB/TrEMBL  Length:267

    Alignment length:265
                                    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     
         Q5SLG2_THET8     1 MVDSHVHTPLCGHAEGHPEAYLEEARAKGLKGVVFTDHSPMPPWYDPESRMRLEALPFYLLALERVRERAQDLYVGIGLEADFHPGTEGFLAQLLRRYPFDYVIGSVHYLGAWPLDHPDHQEEYAWRDLKEVFRAYFQEVEKAARSGLFHAIGHLDLPKKFGHRLPEEALLELAEPALRAVAEAGLFLDVNTAGLRRPAKEVYPAPALLRRARELGIGLVLGSDAHRPEEVGFAFPEVQALLAGLGFREAYYFVEGSPVAYPLSR 265
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -PHP-2yz5B01 B:2-204                                                                                                                                                                                        ----PHP_C-2yz5B03 B:209-244             --------------------- Pfam domains (1)
           Pfam domains (2) -PHP-2yz5B02 B:2-204                                                                                                                                                                                        ----PHP_C-2yz5B04 B:209-244             --------------------- Pfam domains (2)
         Sec.struct. author .eeeee.hhhhh....hhhhhhhhhhhh...eeeeeee.......hhhhh.hhhhhhhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhh......eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee...hhhhh.....hhhhhhhhhhhhhhhhhhhh.eeeeehhhhhh.......hhhhhhhhhhh...eeee....hhhhh..hhhhhhhhhhhh...eeeeee..eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yz5 B   1 MVDSHVHTPLCGHAEGHPEAYLEEARAKGLKGVVFTDHSPMPPWYDPESRMRLEALPFYLLALERVRERAQDLYVGIGLEADFHPGTEGFLAQLLRRYPFDYVIGSVHYLGAWPLDHPDHQEEYAWRDLKEVFRAYFQEVEKAARSGLFHAIGHLDLPKKFGHRLPEEALLELAEPALRAVAEAGLFLDVNTAGLRRPAKEVYPAPALLRRARELGIGLVLGSDAHRPEEVGFAFPEVQALLAGLGFREAYYFVEGSPVAYPLSR 265
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 2YZ5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YZ5)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: Amidohydrolase (126)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5SLG2_THET8 | Q5SLG2)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004401    histidinol-phosphatase activity    Catalysis of the reaction: L-histidinol phosphate + H(2)O = L-histidinol + phosphate.
    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.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0000105    histidine biosynthetic process    The chemical reactions and pathways resulting in the formation of histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Tyr A:203 - Pro A:204   [ RasMol ]  
    Tyr B:203 - Pro B:204   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2yz5
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q5SLG2_THET8 | Q5SLG2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.1.3.15
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q5SLG2_THET8 | Q5SLG2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q5SLG2_THET8 | Q5SLG2: 2yxo 2z4g

(-) Related Entries Specified in the PDB File

2yxo THE SAME PROTEIN COMPLEXED WITH SULFATE
2yz9