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(-) Description

Title :  X-RAY STRUCTURE OF THE ARCHAEOGLOBUS FULGIDUS METHENYL-TETRAHYDROMETHANOPTERIN CYCLOHYDROLASE IN COMPLEX WITH N5-FORMYL-TETRAHYDROMETHANOPTERIN
 
Authors :  V. Upadhyay, U. Demmer, E. Warkentin, J. Moll, S. Shima, U. Ermler
Date :  31 Aug 12  (Deposition) - 31 Oct 12  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  N5-Formyl-Tetrahydromethanopterin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Upadhyay, U. Demmer, E. Warkentin, J. Moll, S. Shima, U. Ermler
Structure And Catalytic Mechanism Of N(5), N(10)-Methenyl-Tetrahydromethanopterin Cyclohydrolase.
Biochemistry V. 51 8435 2012
PubMed-ID: 23013430  |  Reference-DOI: 10.1021/BI300777K

(-) Compounds

Molecule 1 - METHENYLTETRAHYDROMETHANOPTERIN CYCLOHYDROLASE
    Chains: A, B, C
    EC Number: 3.5.4.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-24A(+)
    Expression System Strain: ROSETTA (DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AF_1935, MCH
    Mutation: YES
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 224325
    Strain: DSM 4304
    Synonym: METHENYL-H4MPT CYCLOHYDROLASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1F4M1Ligand/Ion1-[4-({(1R)-1-[(6S,7R)-2-AMINO-5-FORMYL-7-METHYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]ETHYL}AMINO)PHENYL]-1-DEOXY-5-O-{5-O-[(R)-{[(1R)-1,3-DICARBOXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]-ALPHA-D-RIBOFURANOSYL}-D-RIBITOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:94 , ALA B:95 , MET B:107 , GLU B:140 , ILE B:180 , ARG B:183 , GLN B:186 , THR B:187 , PHE B:190 , MET B:222 , ASN B:226 , PHE B:272 , PHE B:280BINDING SITE FOR RESIDUE F4M B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GVS)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Lys A:118 -Pro A:119
2Lys B:118 -Pro B:119
3Lys C:118 -Pro C:119

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GVS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GVS)

(-) Exons   (0, 0)

(no "Exon" information available for 4GVS)

(-) 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:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4gvsa_ A: automated matches                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh.eeee.....eeee.......hhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeee.hhhhhhh......eeeee..eeeeee..hhhhhh.hhhhhhhhh.......eeeeee.....hhhhhhhhhhhhh.hhh.eeeeee...hhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeeee......hhhhhhhhhhhhhhhhheeeeee...hhhhhhhhhhhh......hhhhhhh...hhhhh........eeeeee.....eeeee..hhhhhhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gvs A   1 MLSVNEIAAEIVEDMLDYEEELRIESKKLENGAIVVDCGVNVPGSYDAGIMYTQVCMGGLADVDIVVDTINDVPFAFVTEYTDHPAIACLGSQKAGWQIKVDKYFAMGSGPARALALKPKKTYERIEYEDDADVAVIALEANQLPDEKVMEFIAKECDVDPENVYALVAPTASIVGSVQISGRIVQTAIFKMNEIGYDPKLIVSGAGRCPISPILENDLKAMGSTNDSMMYYGSVFLTVKKYDEILKNVPSCTSRDYGKPFYEIFKAANYDFYKIDPNLFAPAQIAVNDLETGKTYVHGKLNAEVLFQSYQIVLE 315
                                    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     


Chain B from PDB  Type:PROTEIN  Length:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4gvsb_ B: automated matches                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh.eeee.....eeee.......hhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeee.hhhhhhh......eeeee..eeeeee..hhhhhh.hhhhhhhhh.......eeeeee.....hhhhhhhhhhhhh.hhh.eeeeee...hhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeeee......hhhhhhhhhhhhhhhhheeeeee...hhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhh...eeeeee.....eeeee..hhhhhhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gvs B   1 MLSVNEIAAEIVEDMLDYEEELRIESKKLENGAIVVDCGVNVPGSYDAGIMYTQVCMGGLADVDIVVDTINDVPFAFVTEYTDHPAIACLGSQKAGWQIKVDKYFAMGSGPARALALKPKKTYERIEYEDDADVAVIALEANQLPDEKVMEFIAKECDVDPENVYALVAPTASIVGSVQISGRIVQTAIFKMNEIGYDPKLIVSGAGRCPISPILENDLKAMGSTNDSMMYYGSVFLTVKKYDEILKNVPSCTSRDYGKPFYEIFKAANYDFYKIDPNLFAPAQIAVNDLETGKTYVHGKLNAEVLFQSYQIVLE 315
                                    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     


Chain C from PDB  Type:PROTEIN  Length:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4gvsc_ C: automated matches                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh.eeee.....eeee.......hhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeee.hhhhhhh......eeeee..eeeeee..hhhhhh.hhhhhhhhh.......eeeeee.....hhhhhhhhhhhhh.hhh.eeeeee...hhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeeee......hhhhhhhhhhhhhhhhheeeeee...hhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhh...eeeeee.....eeeee..hhhhhhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gvs C   1 MLSVNEIAAEIVEDMLDYEEELRIESKKLENGAIVVDCGVNVPGSYDAGIMYTQVCMGGLADVDIVVDTINDVPFAFVTEYTDHPAIACLGSQKAGWQIKVDKYFAMGSGPARALALKPKKTYERIEYEDDADVAVIALEANQLPDEKVMEFIAKECDVDPENVYALVAPTASIVGSVQISGRIVQTAIFKMNEIGYDPKLIVSGAGRCPISPILENDLKAMGSTNDSMMYYGSVFLTVKKYDEILKNVPSCTSRDYGKPFYEIFKAANYDFYKIDPNLFAPAQIAVNDLETGKTYVHGKLNAEVLFQSYQIVLE 315
                                    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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GVS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GVS)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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    Lys A:118 - Pro A:119   [ RasMol ]  
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 Related Entries

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UniProtKB/Swiss-Prot
        MCH_ARCFU | O28344: 4gvq 4gvr

(-) Related Entries Specified in the PDB File

4gvq 4gvr