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(-) Description

Title :  CRYSTAL STRUCTURE OF 5-METHYLTHIORIBOSE 1-PHOSPHATE ISOMERASE PRODUCT COMPLEX FROM BACILLUS SUBTILIS
 
Authors :  H. Tamura, T. Inoue, Y. Kai, H. Matsumura
Date :  13 Apr 07  (Deposition) - 22 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Isomerase, Methionine Salvage Pathway, Crystal Structure (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Tamura, Y. Saito, H. Ashida, T. Inoue, Y. Kai, A. Yokota, H. Matsumura
Crystal Structure Of 5-Methylthioribose 1-Phosphate Isomerase Product Complex From Bacillus Subtilis: Implications For Catalytic Mechanism
Protein Sci. V. 17 126 2008
PubMed-ID: 18156470  |  Reference-DOI: 10.1110/PS.073169008
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
    Chains: A, B, C, D
    EC Number: 5.3.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MTNA
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: MTR-1-P ISOMERASE, S-METHYL-5-THIORIBOSE-1- PHOSPHATE ISOMERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MRU4Ligand/Ion5-S-METHYL-1-O-PHOSPHONO-5-THIO-D-RIBULOSE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MRU2Ligand/Ion5-S-METHYL-1-O-PHOSPHONO-5-THIO-D-RIBULOSE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MRU2Ligand/Ion5-S-METHYL-1-O-PHOSPHONO-5-THIO-D-RIBULOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:51 , GLY A:52 , ALA A:53 , ARG A:94 , CYS A:160 , ALA A:162 , ALA A:166 , THR A:167 , GLN A:199 , ALA A:239 , ASP A:240 , ASN A:250 , LYS A:251 , PHE A:317BINDING SITE FOR RESIDUE MRU A 501
2AC2SOFTWAREARG B:51 , GLY B:52 , ALA B:53 , PRO B:54 , ILE B:56 , ARG B:94 , CYS B:160 , ALA B:162 , ALA B:166 , GLN B:199 , ALA B:239 , ASP B:240 , ASN B:250 , LYS B:251 , PHE B:317BINDING SITE FOR RESIDUE MRU B 502
3AC3SOFTWAREARG C:51 , GLY C:52 , ALA C:53 , ARG C:94 , CYS C:160 , ALA C:162 , ALA C:166 , THR C:167 , THR C:172 , GLN C:199 , ALA C:239 , ASP C:240 , ASN C:250 , LYS C:251 , HOH C:533BINDING SITE FOR RESIDUE MRU C 503
4AC4SOFTWAREARG D:51 , GLY D:52 , ALA D:53 , PRO D:54 , ARG D:94 , CYS D:160 , ALA D:162 , ALA D:166 , GLN D:199 , ALA D:239 , ASP D:240 , ASN D:250 , LYS D:251 , PHE D:317BINDING SITE FOR RESIDUE MRU D 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Leu A:26 -Pro A:27
2Arg A:195 -Pro A:196
3Leu B:26 -Pro B:27
4Arg B:195 -Pro B:196
5Leu C:26 -Pro C:27
6Arg C:195 -Pro C:196
7Leu D:26 -Pro D:27
8Arg D:195 -Pro D:196

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YVK)

(-) 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:349
 aligned with MTNA_BACSU | O31662 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:349
                                    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         
           MTNA_BACSU     1 MTHSFAVPRSVEWKETAITILNQQKLPDETEYLELTTKEDVFDAIVTLKVRGAPAIGITAAFGLALAAKDIETDNVTEFRRRLEDIKQYLNSSRPTAINLSWALERLSHSVENAISVNEAKTNLVHEAIQIQVEDEETCRLIGQNALQLFKKGDRIMTICNAGSIATSRYGTALAPFYLAKQKDLGLHIYACETRPVLQGSRLTAWELMQGGIDVTLITDSMAAHTMKEKQISAVIVGADRIAKNGDTANKIGTYGLAILANAFDIPFFVAAPLSTFDTKVKCGADIPIEERDPEEVRQISGVRTAPSNVPVFNPAFDITPHDLISGIITEKGIMTGNYEEEIEQLFKG 349
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2yvkA01 A:1-148 translation initiation factor eif-2b, domain 1                                                                                      2yvkA02 A:149-349 Translation initiation factor eif-2b; domain 2                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh...eee....eeee.hhhh.....eeee.hhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee...............hhhhhhhhhh....eeeee.....hhhhhhhhhhhhh...eeeeehhhhhhhhhhhh...eeee...eee....eeee.hhhhhhhhhhhh...eeee.hhh.ee....hhhhh......hhhhhee..ee............eeeehhhhh.eeee..eee..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yvk A   1 MTHSFAVPRSVEWKETAITILNQQKLPDETEYLELTTKEDVFDAIVTLKVRGAPAIGITAAFGLALAAKDIETDNVTEFRRRLEDIKQYLNSSRPTAINLSWALERLSHSVENAISVNEAKTNLVHEAIQIQVEDEETCRLIGQNALQLFKKGDRIMTICNAGSIATSRYGTALAPFYLAKQKDLGLHIYACETRPVLQGSRLTAWELMQGGIDVTLITDSMAAHTMKEKQISAVIVGADRIAKNGDTANKIGTYGLAILANAFDIPFFVAAPLSTFDTKVKCGADIPIEERDPEEVRQISGVRTAPSNVPVFNPAFDITPHDLISGIITEKGIMTGNYEEEIEQLFKG 349
                                    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         


Chain B from PDB  Type:PROTEIN  Length:349
 aligned with MTNA_BACSU | O31662 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:349
                                    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         
           MTNA_BACSU     1 MTHSFAVPRSVEWKETAITILNQQKLPDETEYLELTTKEDVFDAIVTLKVRGAPAIGITAAFGLALAAKDIETDNVTEFRRRLEDIKQYLNSSRPTAINLSWALERLSHSVENAISVNEAKTNLVHEAIQIQVEDEETCRLIGQNALQLFKKGDRIMTICNAGSIATSRYGTALAPFYLAKQKDLGLHIYACETRPVLQGSRLTAWELMQGGIDVTLITDSMAAHTMKEKQISAVIVGADRIAKNGDTANKIGTYGLAILANAFDIPFFVAAPLSTFDTKVKCGADIPIEERDPEEVRQISGVRTAPSNVPVFNPAFDITPHDLISGIITEKGIMTGNYEEEIEQLFKG 349
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2yvkB01 B:1-148 translation initiation factor eif-2b, domain 1                                                                                      2yvkB02 B:149-349 Translation initiation factor eif-2b; domain 2                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...eee....eeee.hhhh.....eeee.hhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee...............hhhhhhhh......eeeee.....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhhh...eeee...eee....eeee.hhhhhhhhhhhh...eeee.hhh.ee....hhhhh......hhhhhee..ee............eeeehhhhh.eee....ee..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yvk B   1 MTHSFAVPRSVEWKETAITILNQQKLPDETEYLELTTKEDVFDAIVTLKVRGAPAIGITAAFGLALAAKDIETDNVTEFRRRLEDIKQYLNSSRPTAINLSWALERLSHSVENAISVNEAKTNLVHEAIQIQVEDEETCRLIGQNALQLFKKGDRIMTICNAGSIATSRYGTALAPFYLAKQKDLGLHIYACETRPVLQGSRLTAWELMQGGIDVTLITDSMAAHTMKEKQISAVIVGADRIAKNGDTANKIGTYGLAILANAFDIPFFVAAPLSTFDTKVKCGADIPIEERDPEEVRQISGVRTAPSNVPVFNPAFDITPHDLISGIITEKGIMTGNYEEEIEQLFKG 349
                                    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         


Chain C from PDB  Type:PROTEIN  Length:349
 aligned with MTNA_BACSU | O31662 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:349
                                    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         
           MTNA_BACSU     1 MTHSFAVPRSVEWKETAITILNQQKLPDETEYLELTTKEDVFDAIVTLKVRGAPAIGITAAFGLALAAKDIETDNVTEFRRRLEDIKQYLNSSRPTAINLSWALERLSHSVENAISVNEAKTNLVHEAIQIQVEDEETCRLIGQNALQLFKKGDRIMTICNAGSIATSRYGTALAPFYLAKQKDLGLHIYACETRPVLQGSRLTAWELMQGGIDVTLITDSMAAHTMKEKQISAVIVGADRIAKNGDTANKIGTYGLAILANAFDIPFFVAAPLSTFDTKVKCGADIPIEERDPEEVRQISGVRTAPSNVPVFNPAFDITPHDLISGIITEKGIMTGNYEEEIEQLFKG 349
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2yvkC01 C:1-148 translation initiation factor eif-2b, domain 1                                                                                      2yvkC02 C:149-349 Translation initiation factor eif-2b; domain 2                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...eee....eeee.hhhh.....eeee.hhhhhhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee...............hhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhh...eeee...eee....eeee.hhhhhhhhhhhh...eeee.hhh.ee....hhhhh......hhhhhee..ee............eeeehhhhh.eeee..eee..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yvk C   1 MTHSFAVPRSVEWKETAITILNQQKLPDETEYLELTTKEDVFDAIVTLKVRGAPAIGITAAFGLALAAKDIETDNVTEFRRRLEDIKQYLNSSRPTAINLSWALERLSHSVENAISVNEAKTNLVHEAIQIQVEDEETCRLIGQNALQLFKKGDRIMTICNAGSIATSRYGTALAPFYLAKQKDLGLHIYACETRPVLQGSRLTAWELMQGGIDVTLITDSMAAHTMKEKQISAVIVGADRIAKNGDTANKIGTYGLAILANAFDIPFFVAAPLSTFDTKVKCGADIPIEERDPEEVRQISGVRTAPSNVPVFNPAFDITPHDLISGIITEKGIMTGNYEEEIEQLFKG 349
                                    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         


Chain D from PDB  Type:PROTEIN  Length:349
 aligned with MTNA_BACSU | O31662 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:349
                                    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         
           MTNA_BACSU     1 MTHSFAVPRSVEWKETAITILNQQKLPDETEYLELTTKEDVFDAIVTLKVRGAPAIGITAAFGLALAAKDIETDNVTEFRRRLEDIKQYLNSSRPTAINLSWALERLSHSVENAISVNEAKTNLVHEAIQIQVEDEETCRLIGQNALQLFKKGDRIMTICNAGSIATSRYGTALAPFYLAKQKDLGLHIYACETRPVLQGSRLTAWELMQGGIDVTLITDSMAAHTMKEKQISAVIVGADRIAKNGDTANKIGTYGLAILANAFDIPFFVAAPLSTFDTKVKCGADIPIEERDPEEVRQISGVRTAPSNVPVFNPAFDITPHDLISGIITEKGIMTGNYEEEIEQLFKG 349
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2yvkD01 D:1-148 translation initiation factor eif-2b, domain 1                                                                                      2yvkD02 D:149-349 Translation initiation factor eif-2b; domain 2                                                                                                                                          CATH domains
           Pfam domains (1) ------------------------------------------------IF-2B-2yvkD01 D:49-337                                                                                                                                                                                                                                                                           ------------ Pfam domains (1)
           Pfam domains (2) ------------------------------------------------IF-2B-2yvkD02 D:49-337                                                                                                                                                                                                                                                                           ------------ Pfam domains (2)
           Pfam domains (3) ------------------------------------------------IF-2B-2yvkD03 D:49-337                                                                                                                                                                                                                                                                           ------------ Pfam domains (3)
           Pfam domains (4) ------------------------------------------------IF-2B-2yvkD04 D:49-337                                                                                                                                                                                                                                                                           ------------ Pfam domains (4)
         Sec.struct. author ..hhhhh...eee....eeee..........eeee.hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee...............hhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhh...eeee...eee....eeee.hhhhhhhhhhhh...eeee.hhh.ee....hhhhh......hhhhhh.................eeeehhhhh.eeee..eee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yvk D   1 MTHSFAVPRSVEWKETAITILNQQKLPDETEYLELTTKEDVFDAIVTLKVRGAPAIGITAAFGLALAAKDIETDNVTEFRRRLEDIKQYLNSSRPTAINLSWALERLSHSVENAISVNEAKTNLVHEAIQIQVEDEETCRLIGQNALQLFKKGDRIMTICNAGSIATSRYGTALAPFYLAKQKDLGLHIYACETRPVLQGSRLTAWELMQGGIDVTLITDSMAAHTMKEKQISAVIVGADRIAKNGDTANKIGTYGLAILANAFDIPFFVAAPLSTFDTKVKCGADIPIEERDPEEVRQISGVRTAPSNVPVFNPAFDITPHDLISGIITEKGIMTGNYEEEIEQLFKG 349
                                    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
   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 2YVK)

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: ISOCOT_Fold (53)
(-)
Family: IF-2B (6)
(-)
Bacillus subtilis (2)
1aIF-2B-2yvkD01D:49-337
1bIF-2B-2yvkD02D:49-337
1cIF-2B-2yvkD03D:49-337
1dIF-2B-2yvkD04D:49-337

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (MTNA_BACSU | O31662)
molecular function
    GO:0046523    S-methyl-5-thioribose-1-phosphate isomerase activity    Catalysis of the reaction: S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-D-ribulose 1-phosphate.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
    GO:0019284    L-methionine salvage from S-adenosylmethionine    The chemical reactions and pathways resulting in the formation of L-methionine from S-adenosylmethionine.
    GO:0019509    L-methionine salvage from methylthioadenosine    The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0044249    cellular biosynthetic process    The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
    GO:0044237    cellular metabolic process    The chemical reactions and pathways by which individual cells transform chemical substances.
    GO:0009086    methionine biosynthetic process    The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  2yvk
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  5.3.1.23
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 Related Entries

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

UniProtKB/Swiss-Prot
        MTNA_BACSU | O31662: 2yrf

(-) Related Entries Specified in the PDB File

2yrf THE SAME PROTEIN COMPLEXED WITH SULFATE ION