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(-) Description

Title :  CRYSTAL STRUCTURE OF THE EUKARYOTIC INITIATION FACTOR 2B FROM LEISHMANIA MAJOR AT 2.1 A RESOLUTION
 
Authors :  J. Bosch, W. G. J. Hol, Structural Genomics Of Pathogenic Protozoa Consortium (Sgpp)
Date :  17 Jun 05  (Deposition) - 02 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sgpp, Structural Genomics, Psi, Protein Structure Initiative, Eukaryotic Initiation Factor, Leishmania, Structural Genomics Of Pathogenic Protozoa Consortium, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Bosch, W. G. J. Hol, Structural Genomics Of Pathogenic Protozoa Consortium (Sgpp
Crystal Structure Of The Eukaryotic Initiation Factor 2B From Leishmania Major At 2. 1 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - INITIATION FACTOR 2B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14B
    Expression System Strain: BL21STAR(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: T7 SYSTEM
    Gene: CHR36_TMP.296
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 19)

Asymmetric/Biological Unit (2, 19)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
2SO410Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:119 , ARG A:266 , HOH A:553BINDING SITE FOR RESIDUE SO4 A 401
02AC2SOFTWAREMSE A:58 , ARG A:61 , GLY A:62 , ARG A:108 , GLN A:224 , LYS A:276 , HOH A:423BINDING SITE FOR RESIDUE SO4 A 402
03AC3SOFTWARETHR A:47 , VAL A:48 , GLU A:49 , LYS A:81 , PHE A:96BINDING SITE FOR RESIDUE SO4 A 403
04AC4SOFTWAREARG A:255 , SER B:340BINDING SITE FOR RESIDUE SO4 A 404
05AC5SOFTWAREARG A:255 , HOH A:427 , TRP B:342BINDING SITE FOR RESIDUE SO4 A 405
06AC6SOFTWARELYS A:12 , LYS A:22 , THR B:47 , VAL B:48 , GLU B:49BINDING SITE FOR RESIDUE SO4 B 406
07AC7SOFTWAREARG B:119 , ARG B:266 , HOH B:519 , HOH B:537 , HOH B:541BINDING SITE FOR RESIDUE SO4 B 407
08AC8SOFTWAREMSE B:58 , ARG B:61 , GLY B:62 , ARG B:108 , GLN B:224 , LYS B:276 , PHE B:346 , HOH B:438BINDING SITE FOR RESIDUE SO4 B 408
09AC9SOFTWARESER A:340 , ARG B:255BINDING SITE FOR RESIDUE SO4 B 409
10BC1SOFTWAREARG B:255BINDING SITE FOR RESIDUE SO4 B 410

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A0U)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Thr A:17 -Leu A:18
2Leu A:36 -Pro A:37
3Leu A:87 -Lys A:88
4Arg A:220 -Pro A:221
5Leu B:36 -Pro B:37
6Arg B:220 -Pro B:221

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A0U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A0U)

(-) Exons   (0, 0)

(no "Exon" information available for 2A0U)

(-) 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:374
 aligned with MTNA_LEIMA | Q4Q0R9 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:374
                                    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       351       361       371    
           MTNA_LEIMA     2 MSKPHHATLESIKYTPGSLRLLDQRKLPLETVFDDVLTVEDIWSAIKEMRVRGAPAIAVSAALGIAVATQRKAANGELKSGREVQTFLLTSCDFVMTSRPTAVNLFNCLRDLKAQVDKLDPTKAAAEVAQAFVELAEAVYTNDVAFNEGIMRHGAAHILAAAKAEGRDKVSILTICNTGALATSRYGTALGVVRQLFYDGKLERVYACETRPWNQGARLTVYECVQEDIPCTLICDGAASSLMLNRKIDAVVVGADRICQNGDTANKIGTYNLAVSAKFHGVKLYVAAPTTTLDVKTASGNHVEIEEREPTEITTNLVTKQRVVADGPHLSIWNPVFDITPSELITGGIITEKGVQAPAASAPYYDIASIIAQA 375
               SCOP domains d2a0ua1 A:10-383 Initiation factor 2b                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -2a0uA01 A:11-176 translation initiation factor eif-2b, domain 1                                                                                                       2a0uA02 A:177-383 Translation initiation factor eif-2b; domain 2                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee..eeeee..........eeee.hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.............hhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhhh...eeeehhhhhhhhhhhh...eeee...ee.....eeee.hhhhhhhhhhhh...eeee.hhhhh.....hhhhh......hhhhhh..............eee....eeeehhhhh..eee....ee.........hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a0u A  10 mSKPHHATLESIKYTPGSLRLLDQRKLPLETVFDDVLTVEDIWSAIKEmRVRGAPAIAVSAALGIAVATQRKAANGELKSGREVQTFLLTSCDFVmTSRPTAVNLFNCLRDLKAQVDKLDPTKAAAEVAQAFVELAEAVYTNDVAFNEGImRHGAAHILAAAKAEGRDKVSILTICNTGALATSRYGTALGVVRQLFYDGKLERVYACETRPWNQGARLTVYECVQEDIPCTLICDGAASSLmLNRKIDAVVVGADRICQNGDTANKIGTYNLAVSAKFHGVKLYVAAPTTTLDVKTASGNHVEIEEREPTEITTNLVTKQRVVADGPHLSIWNPVFDITPSELITGGIITEKGVQAPAASAPYYDIASIIAQA 383
                            |       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       349       359       369       379    
                            |                                              58-MSE                                        105-MSE                                                160-MSE                                                                                     252-MSE                                                                                                                               
                           10-MSE                                                                                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:367
 aligned with MTNA_LEIMA | Q4Q0R9 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:367
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       
           MTNA_LEIMA     9 TLESIKYTPGSLRLLDQRKLPLETVFDDVLTVEDIWSAIKEMRVRGAPAIAVSAALGIAVATQRKAANGELKSGREVQTFLLTSCDFVMTSRPTAVNLFNCLRDLKAQVDKLDPTKAAAEVAQAFVELAEAVYTNDVAFNEGIMRHGAAHILAAAKAEGRDKVSILTICNTGALATSRYGTALGVVRQLFYDGKLERVYACETRPWNQGARLTVYECVQEDIPCTLICDGAASSLMLNRKIDAVVVGADRICQNGDTANKIGTYNLAVSAKFHGVKLYVAAPTTTLDVKTASGNHVEIEEREPTEITTNLVTKQRVVADGPHLSIWNPVFDITPSELITGGIITEKGVQAPAASAPYYDIASIIAQA 375
               SCOP domains d2a0ub_ B: Initiation factor 2b                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2a0uB01 B:17-176 translation initiation factor eif-2b, domain 1                                                                                                 2a0uB02 B:177-383 Translation initiation factor eif-2b; domain 2                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeeee..........eeee.hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.............hhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhhh...eeeehhhhhhhhhhhh...eeee...ee.....eeee.hhhhhhhhhhhh...eeee.hhhhh.....hhhhh......hhhhhh..............eee....eeeehhhhh..eeee..eee.........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a0u B  17 TLESIKYTPGSLRLLDQRKLPLETVFDDVLTVEDIWSAIKEmRVRGAPAIAVSAALGIAVATQRKAANGELKSGREVQTFLLTSCDFVmTSRPTAVNLFNCLRDLKAQVDKLDPTKAAAEVAQAFVELAEAVYTNDVAFNEGImRHGAAHILAAAKAEGRDKVSILTICNTGALATSRYGTALGVVRQLFYDGKLERVYACETRPWNQGARLTVYECVQEDIPCTLICDGAASSLmLNRKIDAVVVGADRICQNGDTANKIGTYNLAVSAKFHGVKLYVAAPTTTLDVKTASGNHVEIEEREPTEITTNLVTKQRVVADGPHLSIWNPVFDITPSELITGGIITEKGVQAPAASAPYYDIASIIAQA 383
                                    26        36        46        56 |      66        76        86        96       106       116       126       136       146       156   |   166       176       186       196       206       216       226       236       246     | 256       266       276       286       296       306       316       326       336       346       356       366       376       
                                                                    58-MSE                                        105-MSE                                                160-MSE                                                                                     252-MSE
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A0U)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MTNA_LEIMA | Q4Q0R9)
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.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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