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(-) Description

Title :  CRYSTAL STRUCTURE OF UNCHARACTERIZED CONSERVED ARCHAEL PROTEIN FROM METHANOPYRUS KANDLERI
 
Authors :  J. B. Bonanno, U. A. Ramagopal, M. Dickey, K. T. Bain, A. Powell, S. Ozyurt, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  18 Sep 06  (Deposition) - 03 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tetramer With Intra-Molecular And Inter-Molecular Disufide Bonds, Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Bonanno, U. A. Ramagopal, M. Dickey, K. T. Bain, A. Powell, S. Ozyurt, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Uncharacterized Conserved Archael Protein From Methanopyrus Kandleri
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN CONSERVED IN ARCHAEA
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MODIFIED PET26
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: Q8TX89_METKA, MK0786
    Organism Scientific: METHANOPYRUS KANDLERI
    Organism Taxid: 2320

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:139 , CYS B:33 , HOH B:161 , CYS C:33 , HOH C:148 , HOH C:165BINDING SITE FOR RESIDUE MG B 1
2AC2SOFTWARECYS A:33 , HOH A:137 , HOH C:160 , CYS D:33 , HOH D:195BINDING SITE FOR RESIDUE MG D 1

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:48 -C:48
2A:58 -A:95
3B:48 -D:48
4B:58 -B:95
5C:58 -C:95
6D:58 -D:95

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IEC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2IEC)

(-) 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:113
 aligned with MPTD_METKA | Q8TX89 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:113
                                    16        26        36        46        56        66        76        86        96       106       116   
           MPTD_METKA     7 LSDRERAIFEAGITLGAIYHQFCGTPVSPGTAEEVAKCIERAALLQPCVIDARVEVDVSSEDTDNYGGYTEVSGRNLRVTIVTRCGEWEAVGKLEFIEELNYPLMWVEEIRRV 119
               SCOP domains d2ieca1 A:11-123 Hypothetical protein MK0786                                                                      SCOP domains
               CATH domains 2iecA00 A:11-123 MK0786-like domain                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhh....eeeeeeee..hhhhhh.....ee.....eeeeeeeee..eeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2iec A  11 LSDRERAIFEAGITLGAIYHQFCGTPVSPGTAEEVAKCIERAALLQPCVIDARVEVDVSSEDTDNYGGYTEVSGRNLRVTIVTRCGEWEAVGKLEFIEELNYPLMWVEEIRRV 123
                                    20        30        40        50        60        70        80        90       100       110       120   


Chain B from PDB  Type:PROTEIN  Length:114
 aligned with MPTD_METKA | Q8TX89 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:116
                                    12        22        32        42        52        62        72        82        92       102       112      
           MPTD_METKA     3 YFKRLSDRERAIFEAGITLGAIYHQFCGTPVSPGTAEEVAKCIERAALLQPCVIDARVEVDVSSEDTDNYGGYTEVSGRNLRVTIVTRCGEWEAVGKLEFIEELNYPLMWVEEIRR 118
               SCOP domains d2iecb_ B: Hypothetical protein MK0786                                                                               SCOP domains
               CATH domains 2iecB00 B:7-122 MK0786-like domain                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh..ee...hhhhhhhhhhhhhhhh..eeeeeeee....--.......ee.....eeeeeeeee..eeeeeeeee......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2iec B   7 YFKRLSDRERAIFEAGITLGAIYHQFCGTPVSPGTAEEVAKCIERAALLQPCVIDARVEVDVSS--TDNYGGYTEVSGRNLRVTIVTRCGEWEAVGKLEFIEELNYPLMWVEEIRR 122
                                    16        26        36        46        56        66   |  | 76        86        96       106       116      
                                                                                          70 73                                                 


Chain C from PDB  Type:PROTEIN  Length:111
 aligned with MPTD_METKA | Q8TX89 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:117
                                    12        22        32        42        52        62        72        82        92       102       112       
           MPTD_METKA     3 YFKRLSDRERAIFEAGITLGAIYHQFCGTPVSPGTAEEVAKCIERAALLQPCVIDARVEVDVSSEDTDNYGGYTEVSGRNLRVTIVTRCGEWEAVGKLEFIEELNYPLMWVEEIRRV 119
               SCOP domains d2iecc_ C: Hypothetical protein MK0786                                                                                SCOP domains
               CATH domains 2iecC00 C:7-123 MK0786-like domain                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh..ee...hhhhhhhhhhhhhh....eeeeeeee..------.....ee.....eeeeeeeee..eeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2iec C   7 YFKRLSDRERAIFEAGITLGAIYHQFCGTPVSPGTAEEVAKCIERAALLQPCVIDARVEVDV------NYGGYTEVSGRNLRVTIVTRCGEWEAVGKLEFIEELNYPLMWVEEIRRV 123
                                    16        26        36        46        56        66 |      76        86        96       106       116       
                                                                                        68     75                                                


Chain D from PDB  Type:PROTEIN  Length:117
 aligned with MPTD_METKA | Q8TX89 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:117
                                    12        22        32        42        52        62        72        82        92       102       112       
           MPTD_METKA     3 YFKRLSDRERAIFEAGITLGAIYHQFCGTPVSPGTAEEVAKCIERAALLQPCVIDARVEVDVSSEDTDNYGGYTEVSGRNLRVTIVTRCGEWEAVGKLEFIEELNYPLMWVEEIRRV 119
               SCOP domains d2iecd_ D: Hypothetical protein MK0786                                                                                SCOP domains
               CATH domains 2iecD00 D:7-123 MK0786-like domain                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh..ee...hhhhhhhhhhhhhh....eeeeeeee..hhhhhh.....ee.....eeeeeeeee..eeeeeeeeeehhhheeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2iec D   7 YFKRLSDRERAIFEAGITLGAIYHQFCGTPVSPGTAEEVAKCIERAALLQPCVIDARVEVDVSSEDTDNYGGYTEVSGRNLRVTIVTRCGEWEAVGKLEFIEELNYPLMWVEEIRRV 123
                                    16        26        36        46        56        66        76        86        96       106       116
   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, 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 2IEC)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (MPTD_METKA | Q8TX89)
molecular function
    GO:0004150    dihydroneopterin aldolase activity    Catalysis of the reaction: 2-amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8-dihydropteridine = 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine + glycolaldehyde.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:2001118    tetrahydromethanopterin biosynthetic process    The chemical reactions and pathways resulting in the formation of a tetrahydromethanopterin.

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(-) Related Entries Specified in the PDB File

2i52 NYSGXRC PSI-2 TARGET RELATED ID: NYSGXRC-10163B RELATED DB: TARGETDB