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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TRANSLATION INITIATION FACTOR EIF-2B, SUBUNIT DELTA, FROM A. FULGIDUS
 
Authors :  V. N. Malashkevich, S. C. Almo, S. K. Burley, New York Sgx Research C Structural Genomics (Nysgxrc)
Date :  04 May 04  (Deposition) - 31 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Translation Initiation Factor, Subunit Delta, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, S. C. Almo
Crystal Structure Of The Translation Initiation Factor Eif-2B, Subunit Delta, From A. Fulgidus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSLATION INITIATION FACTOR EIF2B, SUBUNIT DELTA
    Chains: A, B, C, D
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 224325
    Other Details: GENE EIF2BD
    Strain: DSM 4304
    Synonym: EIF2BD

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1T5O)

(-) Sites  (0, 0)

(no "Site" information available for 1T5O)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:292 -B:292
2C:292 -D:292

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Leu A:20 -Pro A:21
2Arg A:189 -Pro A:190
3Pro A:329 -Pro A:330
4Leu B:20 -Pro B:21
5Arg B:189 -Pro B:190
6Pro B:329 -Pro B:330
7Leu C:20 -Pro C:21
8Arg C:189 -Pro C:190
9Pro C:329 -Pro C:330
10Leu D:20 -Pro D:21
11Arg D:189 -Pro D:190
12Pro D:329 -Pro D:330

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T5O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T5O)

(-) Exons   (0, 0)

(no "Exon" information available for 1T5O)

(-) 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:340
 aligned with MTNA_ARCFU | O29877 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:340
                             1                                                                                                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339
           MTNA_ARCFU     - -MRSIFWDDGLKLIDQTKLPEKLEVIECRNVEELADAIKKLAVRGAPALEAAGAYGIALAAREREFADVDELKEHLKKAADFLASTRPTAVNLFVGIERALNAALKGESVEEVKELALREAEKLAEEDVERNRKMGEYGAELLEDGDVVLTYCNAGRLATVDWGTALGVVRSAVEQGKEIRVIACETRPLNQGSRLTCWELMEDGIDVTLITDSMVGIVMQKGMVDKVIVGADRIVRDAVFNKIGTYTVSVVAKHHNIPFYVAAPKATFDWERTAKDVVIEERPREELIFCGKRQIAPLNVKVYNPAFDPTPLENVTALITEYGVIYPPYEVNVPKVLKF 339
               SCOP domains d1t5oa_ A: Putative eIF-2B delta-subunit                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1t5oA01 A:2-142 translation initiation factor eif-2b, domain 1                                                                               1t5oA02 A:143-341 Translation initiation factor eif-2b; domain 2                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...eeee.hhhh.....eeee.hhhhhhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee.............hhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhh....eeee...eee..eeeee.hhhhhhhhhhhh...eeee.hhhhh....hhhhh......hhhhhee..ee......ee....eeeee.hhh.eeee..eee..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t5o A   2 SLRSIFWDDGLKLIDQTKLPEKLEVIECRNVEELADAIKKLAVRGAPALEAAGAYGIALAAREREFADVDELKEHLKKAADFLASTRPTAVNLFVGIERALNAALKGESVEEVKELALREAEKLAEEDVERNRKMGEYGAELLEDGDVVLTYCNAGRLATVDWGTALGVVRSAVEQGKEIRVIACETRPLNQGSRLTCWELMEDGIDVTLITDSMVGIVMQKGMVDKVIVGADRIVRDAVFNKIGTYTVSVVAKHHNIPFYVAAPKATFDWERTAKDVVIEERPREELIFCGKRQIAPLNVKVYNPAFDPTPLENVTALITEYGVIYPPYEVNVPKVLKF 341
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341


Chain B from PDB  Type:PROTEIN  Length:340
 aligned with MTNA_ARCFU | O29877 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:340
                             1                                                                                                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339
           MTNA_ARCFU     - -MRSIFWDDGLKLIDQTKLPEKLEVIECRNVEELADAIKKLAVRGAPALEAAGAYGIALAAREREFADVDELKEHLKKAADFLASTRPTAVNLFVGIERALNAALKGESVEEVKELALREAEKLAEEDVERNRKMGEYGAELLEDGDVVLTYCNAGRLATVDWGTALGVVRSAVEQGKEIRVIACETRPLNQGSRLTCWELMEDGIDVTLITDSMVGIVMQKGMVDKVIVGADRIVRDAVFNKIGTYTVSVVAKHHNIPFYVAAPKATFDWERTAKDVVIEERPREELIFCGKRQIAPLNVKVYNPAFDPTPLENVTALITEYGVIYPPYEVNVPKVLKF 339
               SCOP domains d1t5ob_ B: Putative eIF-2B delta-subunit                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1t5oB01 B:2-142 translation initiation factor eif-2b, domain 1                                                                               1t5oB02 B:143-341 Translation initiation factor eif-2b; domain 2                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...eeee.hhhh.....eeee.hhhhhhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.............hhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhh...eeeehhhhhhhhhhh....eeee...eee..eeeee.hhhhhhhhhhhh...eeee.hhhhh....hhhhh......hhhhhee..ee......ee....eeeee.hhh.eeee..eee..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t5o B   2 SLRSIFWDDGLKLIDQTKLPEKLEVIECRNVEELADAIKKLAVRGAPALEAAGAYGIALAAREREFADVDELKEHLKKAADFLASTRPTAVNLFVGIERALNAALKGESVEEVKELALREAEKLAEEDVERNRKMGEYGAELLEDGDVVLTYCNAGRLATVDWGTALGVVRSAVEQGKEIRVIACETRPLNQGSRLTCWELMEDGIDVTLITDSMVGIVMQKGMVDKVIVGADRIVRDAVFNKIGTYTVSVVAKHHNIPFYVAAPKATFDWERTAKDVVIEERPREELIFCGKRQIAPLNVKVYNPAFDPTPLENVTALITEYGVIYPPYEVNVPKVLKF 341
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341


Chain C from PDB  Type:PROTEIN  Length:340
 aligned with MTNA_ARCFU | O29877 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:340
                             1                                                                                                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339
           MTNA_ARCFU     - -MRSIFWDDGLKLIDQTKLPEKLEVIECRNVEELADAIKKLAVRGAPALEAAGAYGIALAAREREFADVDELKEHLKKAADFLASTRPTAVNLFVGIERALNAALKGESVEEVKELALREAEKLAEEDVERNRKMGEYGAELLEDGDVVLTYCNAGRLATVDWGTALGVVRSAVEQGKEIRVIACETRPLNQGSRLTCWELMEDGIDVTLITDSMVGIVMQKGMVDKVIVGADRIVRDAVFNKIGTYTVSVVAKHHNIPFYVAAPKATFDWERTAKDVVIEERPREELIFCGKRQIAPLNVKVYNPAFDPTPLENVTALITEYGVIYPPYEVNVPKVLKF 339
               SCOP domains d1t5oc_ C: Putative eIF-2B delta-subunit                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1t5oC01 C:2-142 translation initiation factor eif-2b, domain 1                                                                               1t5oC02 C:143-341 Translation initiation factor eif-2b; domain 2                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...eeee.hhhh.....eeee.hhhhhhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.............hhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhh...eeeehhhhhhhhhhh....eeee...ee...eeeee.hhhhhhhhhhhh...eeee.hhhhh....hhhhh......hhhhhee..ee......ee....eeeee.hhh.eeee..eee..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t5o C   2 SLRSIFWDDGLKLIDQTKLPEKLEVIECRNVEELADAIKKLAVRGAPALEAAGAYGIALAAREREFADVDELKEHLKKAADFLASTRPTAVNLFVGIERALNAALKGESVEEVKELALREAEKLAEEDVERNRKMGEYGAELLEDGDVVLTYCNAGRLATVDWGTALGVVRSAVEQGKEIRVIACETRPLNQGSRLTCWELMEDGIDVTLITDSMVGIVMQKGMVDKVIVGADRIVRDAVFNKIGTYTVSVVAKHHNIPFYVAAPKATFDWERTAKDVVIEERPREELIFCGKRQIAPLNVKVYNPAFDPTPLENVTALITEYGVIYPPYEVNVPKVLKF 341
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341


Chain D from PDB  Type:PROTEIN  Length:340
 aligned with MTNA_ARCFU | O29877 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:340
                             1                                                                                                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339
           MTNA_ARCFU     - -MRSIFWDDGLKLIDQTKLPEKLEVIECRNVEELADAIKKLAVRGAPALEAAGAYGIALAAREREFADVDELKEHLKKAADFLASTRPTAVNLFVGIERALNAALKGESVEEVKELALREAEKLAEEDVERNRKMGEYGAELLEDGDVVLTYCNAGRLATVDWGTALGVVRSAVEQGKEIRVIACETRPLNQGSRLTCWELMEDGIDVTLITDSMVGIVMQKGMVDKVIVGADRIVRDAVFNKIGTYTVSVVAKHHNIPFYVAAPKATFDWERTAKDVVIEERPREELIFCGKRQIAPLNVKVYNPAFDPTPLENVTALITEYGVIYPPYEVNVPKVLKF 339
               SCOP domains d1t5od_ D: Putative eIF-2B delta-subunit                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1t5oD01 D:2-142 translation initiation factor eif-2b, domain 1                                                                               1t5oD02 D:143-341 Translation initiation factor eif-2b; domain 2                                                                                                                                        CATH domains
           Pfam domains (1) -----------------------------------------IF-2B-1t5oD01 D:43-329                                                                                                                                                                                                                                                                         ------------ Pfam domains (1)
           Pfam domains (2) -----------------------------------------IF-2B-1t5oD02 D:43-329                                                                                                                                                                                                                                                                         ------------ Pfam domains (2)
           Pfam domains (3) -----------------------------------------IF-2B-1t5oD03 D:43-329                                                                                                                                                                                                                                                                         ------------ Pfam domains (3)
           Pfam domains (4) -----------------------------------------IF-2B-1t5oD04 D:43-329                                                                                                                                                                                                                                                                         ------------ Pfam domains (4)
         Sec.struct. author ....eee...eeee.hhhh.....eee..hhhhhhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee.............hhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh..eeeehhhhhhhhhhh....eeee...eee..eeeee.hhhhhhhhhhhh...eeee.hhhhh....hhhhh......hhhhhee..ee......ee....eeeee.hhh.eeee..eee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t5o D   2 SLRSIFWDDGLKLIDQTKLPEKLEVIECRNVEELADAIKKLAVRGAPALEAAGAYGIALAAREREFADVDELKEHLKKAADFLASTRPTAVNLFVGIERALNAALKGESVEEVKELALREAEKLAEEDVERNRKMGEYGAELLEDGDVVLTYCNAGRLATVDWGTALGVVRSAVEQGKEIRVIACETRPLNQGSRLTCWELMEDGIDVTLITDSMVGIVMQKGMVDKVIVGADRIVRDAVFNKIGTYTVSVVAKHHNIPFYVAAPKATFDWERTAKDVVIEERPREELIFCGKRQIAPLNVKVYNPAFDPTPLENVTALITEYGVIYPPYEVNVPKVLKF 341
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341
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  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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: ISOCOT_Fold (53)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (MTNA_ARCFU | O29877)
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: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.

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 Related Entries

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