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(-) Description

Title :  CRYSTAL STRUCTURE OF AN HYPOTHETICAL PROTEIN
 
Authors :  Structural Genomix
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622  |  Reference-DOI: 10.1002/PROT.20541

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YQEU
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YQEU, BSU25440
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1VHK)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VHK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VHK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VHK)

(-) 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:235
 aligned with RSME_BACSU | P54461 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:252
                                    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  
           RSME_BACSU     2 QRYFIELTKQQIEEAPTFSITGEEVHHIVNVMRMNEGDQIICCSQDGFEAKCELQSVSKDKVSCLVIEWTNENRELPIKVYIASGLPKGDKLEWIIQKGTELGAHAFIPFQAARSVVKLDDKKAKKKRERWTKIAKEAAEQSYRNEVPRVMDVHSFQQLLQRMQDFDKCVVAYEESSKQGEISAFSAIVSSLPKGSSLLIVFGPEGGLTEAEVERLTEQDGVTCGLGPRILRTETAPLYALSAISYQTELLR 253
               SCOP domains d1vhka1 A:2-73 Hypothetical protein YqeU                                d1vhka2 A:74-253 Hypothetical protein YqeU                                                                                                                                           SCOP domains
               CATH domains 1vhkA01 A:2-74 Hypothetical PUA domain-like; domain 1                    1vhkA02 A:75-253  [code=3.40.1280.10, no nam         e defined]                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee...hhhhhhh...eeeehhhhhhhhh........eeeee.....eeeeeeeee...eeeeeeeee.........eeeeeee....hhhhhhhhhhhhh...eeeee.......---------hhhhhhhhhhhhhhhh......ee....hhhhhhhhhhhh.eeeee..--------hhhhhhhhh.....eeeeee......hhhhhhhhhhh..eee..........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vhk A   2 QRYFIELTKQQIEEAPTFSITGEEVHHIVNVmRmNEGDQIICCSQDGFEAKCELQSVSKDKVSCLVIEWTNENRELPIKVYIASGLPKGDKLEWIIQKGTELGAHAFIPFQAARSVV---------KRERWTKIAKEAAEQSYRNEVPRVmDVHSFQQLLQRmQDFDKCVVAYE--------SAFSAIVSSLPKGSSLLIVFGPEGGLTEAEVERLTEQDGVTCGLGPRILRTETAPLYALSAISYQTELLR 253
                                    11        21        31 | |    41        51        61        71        81        91       101       111      |  -      |131       141       151|      161  |    171   |     -  |    191       201       211       221       231       241       251  
                                                          33-MSE                                                                              118       128                     152-MSE     164-MSE    175      184                                                                     
                                                            35-MSE                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:196
 aligned with RSME_BACSU | P54461 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:252
                                    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  
           RSME_BACSU     2 QRYFIELTKQQIEEAPTFSITGEEVHHIVNVMRMNEGDQIICCSQDGFEAKCELQSVSKDKVSCLVIEWTNENRELPIKVYIASGLPKGDKLEWIIQKGTELGAHAFIPFQAARSVVKLDDKKAKKKRERWTKIAKEAAEQSYRNEVPRVMDVHSFQQLLQRMQDFDKCVVAYEESSKQGEISAFSAIVSSLPKGSSLLIVFGPEGGLTEAEVERLTEQDGVTCGLGPRILRTETAPLYALSAISYQTELLR 253
               SCOP domains d1vhkb1 B                             :2-73 Hypothet           ical protd1vhkb2 B:74-253 Hypothetical protein YqeU                                                                                                                                           SCOP domains
               CATH domains 1vhkB00 B                             :2-253  [code=           3.40.1280.10, no name defined]                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee.....-----------------------------.eeee.....eeee-----------....ee.........eeeeeee....hhhhhhhhhhhhh...eeeee.......----------hhhhhhhhhhhhhhhh.....ee....hhhhhhhhhhhh.eeeee....------.hhhhhhhhh....eeeeee......hhhhhhhhhhh..eee..........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vhk B   2 QRYFIELTK-----------------------------QIICCSQDGFEAKC-----------CLVIEWTNENRELPIKVYIASGLPKGDKLEWIIQKGTELGAHAFIPFQAARSVV----------RERWTKIAKEAAEQSYRNEVPRVmDVHSFQQLLQRmQDFDKCVVAYEES------SAFSAIVSSLPKGSSLLIVFGPEGGLTEAEVERLTEQDGVTCGLGPRILRTETAPLYALSAISYQTELLR 253
                                    |-         -         -        41        51 |       -   |    71        81        91       101       111      |  -       131       141       151|      161  |    171     |   -  |    191       201       211       221       231       241       251  
                                   10                            40           53          65                                                  118        129                    152-MSE     164-MSE      177    184                                                                     


Chain C from PDB  Type:PROTEIN  Length:244
 aligned with RSME_BACSU | P54461 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:252
                                    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  
           RSME_BACSU     2 QRYFIELTKQQIEEAPTFSITGEEVHHIVNVMRMNEGDQIICCSQDGFEAKCELQSVSKDKVSCLVIEWTNENRELPIKVYIASGLPKGDKLEWIIQKGTELGAHAFIPFQAARSVVKLDDKKAKKKRERWTKIAKEAAEQSYRNEVPRVMDVHSFQQLLQRMQDFDKCVVAYEESSKQGEISAFSAIVSSLPKGSSLLIVFGPEGGLTEAEVERLTEQDGVTCGLGPRILRTETAPLYALSAISYQTELLR 253
               SCOP domains d1vhkc1 C:2-73 Hypothetical protein YqeU                                d1vhkc2 C:74-253 Hypothetical protein YqeU                                                                                                                                           SCOP domains
               CATH domains 1vhkC01 C:2-74 Hypothetical PUA domain-like; domain 1                    1vhkC02 C:75-253  [code=3.40.1280.10, no name defined]                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee...hhhhhhhh..eee.hhhhhhhhh........eeeee.....eeeeeeeeee..eeeeeeeee.........eeeeeee....hhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhhhhhhhh.....ee....hhhhhhhhhh...eeeee..--------hhhhhhhhhh....eeeeee......hhhhhhhhhh...eee..........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vhk C   2 QRYFIELTKQQIEEAPTFSITGEEVHHIVNVmRmNEGDQIICCSQDGFEAKCELQSVSKDKVSCLVIEWTNENRELPIKVYIASGLPKGDKLEWIIQKGTELGAHAFIPFQAARSVVKLDDKKAKKKRERWTKIAKEAAEQSYRNEVPRVmDVHSFQQLLQRmQDFDKCVVAYE--------SAFSAIVSSLPKGSSLLIVFGPEGGLTEAEVERLTEQDGVTCGLGPRILRTETAPLYALSAISYQTELLR 253
                                    11        21        31 | |    41        51        61        71        81        91       101       111       121       131       141       151|      161  |    171   |     -  |    191       201       211       221       231       241       251  
                                                          33-MSE                                                                                                                152-MSE     164-MSE    175      184                                                                     
                                                            35-MSE                                                                                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:178
 aligned with RSME_BACSU | P54461 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:252
                                    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  
           RSME_BACSU     2 QRYFIELTKQQIEEAPTFSITGEEVHHIVNVMRMNEGDQIICCSQDGFEAKCELQSVSKDKVSCLVIEWTNENRELPIKVYIASGLPKGDKLEWIIQKGTELGAHAFIPFQAARSVVKLDDKKAKKKRERWTKIAKEAAEQSYRNEVPRVMDVHSFQQLLQRMQDFDKCVVAYEESSKQGEISAFSAIVSSLPKGSSLLIVFGPEGGLTEAEVERLTEQDGVTCGLGPRILRTETAPLYALSAISYQTELLR 253
               SCOP domains d1vhk                                    d1 D:2-73                      d1vhkd2 D:74-253 Hypothetical protein YqeU                                                                                                                                           SCOP domains
               CATH domains 1vhkD                                    00 D:2-25                     3  [code=3.40.1280.10, no name defined]                                                                                                                                               CATH domains
           Pfam domains (1) -----                                    Methyltra                     ns_RNA-1vhkD01 D:43-247                                                                                                                                                        ------ Pfam domains (1)
           Pfam domains (2) -----                                    Methyltra                     ns_RNA-1vhkD02 D:43-247                                                                                                                                                        ------ Pfam domains (2)
           Pfam domains (3) -----                                    Methyltra                     ns_RNA-1vhkD03 D:43-247                                                                                                                                                        ------ Pfam domains (3)
           Pfam domains (4) -----                                    Methyltra                     ns_RNA-1vhkD04 D:43-247                                                                                                                                                        ------ Pfam domains (4)
         Sec.struct. author ...ee------------------------------------.ee......---------------------.......eeeeeee....hhhhhhhhhhhhh...eeeee......----------hhhhhhhhhhhhhhhhh.....ee....hhhhhhhhhhhh.eeeee...-------hhhhhhhhh.....eeeeee......hhhhhhhhhhh..eee..........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vhk D   2 QRYFI------------------------------------CCSQDGFEA---------------------ENRELPIKVYIASGLPKGDKLEWIIQKGTELGAHAFIPFQAARSV----------KRERWTKIAKEAAEQSYRNEVPRVmDVHSFQQLLQRmQDFDKCVVAYEE-------SAFSAIVSSLPKGSSLLIVFGPEGGLTEAEVERLTEQDGVTCGLGPRILRTETAPLYALSAISYQTELLR 253
                                |    -         -         -         - |      51         -         - |      81        91       101       111     |   -      |131       141       151|      161  |    171    |    -  |    191       201       211       221       231       241       251  
                                6                                   43      51                    73                                         117        128                     152-MSE     164-MSE     176     184
   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  (2, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: SPOUT (28)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (RSME_BACSU | P54461)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0070042    rRNA (uridine-N3-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N3-methyluridine.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0070475    rRNA base methylation    The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue in an rRNA molecule.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
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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  1vhk
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 Related Entries

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

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