Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
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 :  THE CRYSTAL STRUCTURE OF METHENYLTETRAHYDROMETHANOPTERIN CYCLOHYDROLASE FROM THE HYPERTHERMOPHILIC ARCHAEON METHANOPYRUS KANDLERI
 
Authors :  W. Grabarse
Date :  01 Sep 99  (Deposition) - 20 Sep 99  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Methanogenesis, Biological Methanogenesis, Hydrolase, Tetrahydromethanopterin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Grabarse, M. Vaupel, J. A. Vorholt, S. Shima, R. K. Thauer, A. Wittershagen, G. Bourenkov, H. D. Bartunik, U. Ermler
The Crystal Structure Of Methenyltetrahydromethano- Pterin Cyclohydrolase From The Hyperthermophilic Archaeon Methanopyrus Kandleri
Structure V. 7 1257 1999
PubMed-ID: 10545331  |  Reference-DOI: 10.1016/S0969-2126(00)80059-3

(-) Compounds

Molecule 1 - METHENYLTETRAHYDROMETHANOPTERIN CYCLOHYDROLASE
    Chains: A
    EC Number: 3.5.4.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cellular Location: CYTOPLASM
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: METHANOPYRUS KANDLERI
    Organism Taxid: 2320
    Other Details: THREE PHOSPHATE MOLECULES
    Other Details - Source: HETEROLOGOUSLY EXPRESSED IN ESCHERICHIA COLI
    Synonym: METHENYL-H4MPT CYCLOHYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 9)
No.NameCountTypeFull Name
1PO49Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:94 , ALA A:95 , ARG A:183 , GLU A:186 , HOH A:2097 , HOH A:2206 , HOH A:2207 , HOH A:2208BINDING SITE FOR RESIDUE PO4 A 400
2AC2SOFTWARETRP A:97 , LYS A:118 , HIS A:152 , GLU A:156 , HOH A:2209 , HOH A:2210BINDING SITE FOR RESIDUE PO4 A 401
3AC3SOFTWAREHIS A:84 , VAL A:87 , HOH A:2022 , HOH A:2211 , HOH A:2212 , HOH A:2213 , HOH A:2214BINDING SITE FOR RESIDUE PO4 A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QLM)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:118 -Pro A:119

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QLM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QLM)

(-) Exons   (0, 0)

(no "Exon" information available for 1QLM)

(-) 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:316
 aligned with MCH_METKA | P94954 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:316
                                    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      
            MCH_METKA     1 MVSVNENALPLVERMIERAELLNVEVQELENGTTVIDCGVEAAGGFEAGLLFSEVCMGGLATVELTEFEHDGLCLPAVQVTTDHPAVSTLAAQKAGWQVQVGDYFAMGSGPARALALKPKETYEEIDYEDDADVAILCLESSELPDEDVAEHVADECGVDPENLYLLVAPTASIVGSVQVSARVVETGLYKLLEVLEYDVTRVKYATGTAPIAPVADDDGEAMGRTNDCILYGGTVYLYVEGDDELPEVVEELPSEASEDYGKPFMKIFEEADYDFYKIDPGVFAPARVVVNDLSTGKTYTAGEINVDVLKESFGL 316
               SCOP domains d1qlma_ A: Methenyltetrahydromethanopterin cyclohydrolase                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1qlmA01 A:1-44,A:96-169                     1qlmA02 A:45-95,A:170-316                          1qlmA01 A:1-44,A:96-169                                                   1qlmA02 A:45-95,A:170-316 Methenyltetrahydromethanopterin Cyclohydrolase; Chain A, domain 2                                                         CATH domains
               Pfam domains --MCH-1qlmA01 A:3-314                                                                                                                                                                                                                                                                                                     -- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh.eeee.....eeee.......hhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeee.hhhhhhh......eeeee..eeeeee..hhhhhh.hhhhhhhhh.......eeeeee.....hhhhhhhhhhhhh.hhh.eeeeee...hhhhhhhhhhhhhhhhhhhhhhh...hhh.eeeeeeeee......hhhhhhhhhhhhhhhhheeeeee....hhhhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhh...eeeee......eeeee..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qlm A   1 MVSVNENALPLVERMIERAELLNVEVQELENGTTVIDCGVEAAGGFEAGLLFSEVCMGGLATVELTEFEHDGLCLPAVQVTTDHPAVSTLAAQKAGWQVQVGDYFAMGSGPARALALKPKETYEEIDYEDDADVAILCLESSELPDEDVAEHVADECGVDPENLYLLVAPTASIVGSVQVSARVVETGLYKLLEVLEYDVTRVKYATGTAPIAPVADDDGEAMGRTNDCILYGGTVYLYVEGDDELPEVVEELPSEASEDYGKPFMKIFEEADYDFYKIDPGVFAPARVVVNDLSTGKTYTAGEINVDVLKESFSL 316
                                    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
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: MCH] (1)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (MCH_METKA | P94954)
molecular function
    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:0018759    methenyltetrahydromethanopterin cyclohydrolase activity    Catalysis of the reaction: 5,10-methenyl-5,6,7,8-tetrahydromethanopterin + H(2)O = N(5)-formyl-5,6,7,8-tetrahydromethanopterin + H(+).
biological process
    GO:0015948    methanogenesis    The chemical reactions and pathways resulting in the formation of methane, a colorless, odorless, flammable gas with the formula CH4. It is the simplest of the alkanes.
    GO:0019386    methanogenesis, from carbon dioxide    The chemical reactions and pathways resulting in the formation of methane, a colorless, odorless, flammable gas with the formula CH4, from other compounds, including carbon dioxide (CO2).
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:118 - Pro A:119   [ 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
  1qlm
    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
  MCH_METKA | P94954
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.5.4.27
    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
  MCH_METKA | P94954
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1QLM)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QLM)