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(-) Description

Title :  THE CRYSTAL STRUCTURE OF YCGJ PROTEIN FROM BACILLUS SUBITILIS
 
Authors :  T. Burke, J. Gorman, L. Shapiro, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  05 Apr 06  (Deposition) - 18 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.91
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nysgxrc, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Burke, J. Gorman, L. Shapiro
The Crystal Structure Of Ycgj Protein From Bacillus Subitilis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - YCGJ
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MODIFIED PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: YCGJ
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric Unit (3, 19)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SAM2Ligand/IonS-ADENOSYLMETHIONINE
3SO411Ligand/IonSULFATE ION
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
3SO44Ligand/IonSULFATE ION
Biological Unit 2 (3, 11)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
3SO47Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:-2 , HIS A:-3 , HIS A:25 , ARG A:85 , HOH A:434BINDING SITE FOR RESIDUE SO4 A 402
02AC2SOFTWAREHIS A:-1 , HIS A:-2 , HIS A:-3 , SER A:0 , TYR A:86 , TRP A:165 , LEU A:167BINDING SITE FOR RESIDUE SO4 A 404
03AC3SOFTWARETYR A:86 , HIS A:89 , HIS A:90 , ASP A:136 , SAM A:301BINDING SITE FOR RESIDUE SO4 A 406
04AC4SOFTWAREHIS A:-2 , PRO B:119 , GLU B:120 , ASP B:121BINDING SITE FOR RESIDUE SO4 A 410
05AC5SOFTWAREHIS B:-3 , HIS B:-1 , SER B:0 , TYR B:86 , TRP B:165BINDING SITE FOR RESIDUE SO4 B 401
06AC6SOFTWAREHIS B:-3 , HIS B:-2 , LEU B:1 , ARG B:85BINDING SITE FOR RESIDUE SO4 B 403
07AC7SOFTWAREHIS B:-3 , ARG B:135 , TRP B:174 , ARG B:177BINDING SITE FOR RESIDUE SO4 B 405
08AC8SOFTWAREASP B:108 , ARG B:184 , ARG B:228BINDING SITE FOR RESIDUE SO4 B 407
09AC9SOFTWAREARG B:11 , PRO B:137 , ARG B:184BINDING SITE FOR RESIDUE SO4 B 408
10BC1SOFTWARETYR B:86 , HIS B:89 , HIS B:90 , ASP B:136 , SAM B:302BINDING SITE FOR RESIDUE SO4 B 409
11BC2SOFTWAREARG B:141 , GLU B:147 , HOH B:419BINDING SITE FOR RESIDUE SO4 B 411
12BC3SOFTWAREGLY A:20 , ALA A:21 , GLY A:22 , THR A:26 , ASP A:41 , ALA A:42 , THR A:43 , MSE A:46 , THR A:68 , ALA A:69 , GLU A:70 , ARG A:85 , TYR A:86 , HIS A:90 , SO4 A:406 , HOH A:435BINDING SITE FOR RESIDUE SAM A 301
13BC4SOFTWAREGLY B:20 , GLY B:22 , HIS B:25 , THR B:26 , ASP B:41 , ALA B:42 , THR B:43 , GLY B:67 , THR B:68 , ALA B:69 , GLU B:70 , ARG B:85 , TYR B:86 , HIS B:90 , PHE B:91 , SO4 B:409BINDING SITE FOR RESIDUE SAM B 302

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:204 -B:217

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GLU)

(-) 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:234
 aligned with YCGJ_BACSU | O31474 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:234
                                                                                                                                                                                                                                                                 253  
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251 |  
           YCGJ_BACSU    22 EGEDLGLMIKTAECRAEHRVLDIGAGAGHTALAFSPYVQECIGVDATKEMVEVASSFAQEKGVENVRFQQGTAESLPFPDDSFDIITCRYAAHHFSDVRKAVREVARVLKQDGRFLLVDHYAPEDPVLDEFVNHLNRLRDPSHVRESSLSEWQAMFSANQLAYQDIQKWNLPIQYDSWIKRGGTPADREKQIITHLNHASDEARDTFCITLNQNGQPISFCLKAILIQGIKR--   -
               SCOP domains -----d2glua1 A:2-228 Hypothetical protein YcgJ                                                                                                                                                                                          -- SCOP domains
               CATH domains 2gluA00 A:-3-230 Vaccinia Virus protein VP39                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhh....eeeee.hhhhh........eeeee.hhhhh.hhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.eeeeeeeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhh..ee.....eeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2glu A  -3 HHHSLGLmIKTAECRAEHRVLDIGAGAGHTALAFSPYVQECIGVDATKEmVEVASSFAQEKGVENVRFQQGTAESLPFPDDSFDIITCRYAAHHFSDVRKAVREVARVLKQDGRFLLVDHYAPEDPVLDEFVNHLNRLRDPSHVRESSLSEWQAmFSANQLAYQDIQKWNLPIQYDSWIKRGGTPADREKQIITHLNHASDEARDTFCITLNQNGQPISFCLKAILIQGIKREG 230
                                   | 6        16        26        36        46        56        66        76        86        96       106       116       126       136       146    |  156       166       176       186       196       206       216       226    
                                   4-MSE                                    46-MSE                                                                                                  151-MSE                                                                           


Chain B from PDB  Type:PROTEIN  Length:234
 aligned with YCGJ_BACSU | O31474 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:234
                                                                                                                                                                                                                                                                 253  
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251 |  
           YCGJ_BACSU    22 EGEDLGLMIKTAECRAEHRVLDIGAGAGHTALAFSPYVQECIGVDATKEMVEVASSFAQEKGVENVRFQQGTAESLPFPDDSFDIITCRYAAHHFSDVRKAVREVARVLKQDGRFLLVDHYAPEDPVLDEFVNHLNRLRDPSHVRESSLSEWQAMFSANQLAYQDIQKWNLPIQYDSWIKRGGTPADREKQIITHLNHASDEARDTFCITLNQNGQPISFCLKAILIQGIKR--   -
               SCOP domains d2glub_ B: Hypothetical protein YcgJ                                                                                                                                                                                                       SCOP domains
               CATH domains 2gluB00 B:-3-230 Vaccinia Virus protein VP39                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhh....eeeee.hhhhh......eeeeeee.hhhhh.hhhhhhhhhhhheeeeeeeeeeee....hhhhhhhhhhhhhhhh.......hhhhhhhhhhh..eeeeeeeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhh..ee.....eeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2glu B  -3 HHHSLGLmIKTAECRAEHRVLDIGAGAGHTALAFSPYVQECIGVDATKEmVEVASSFAQEKGVENVRFQQGTAESLPFPDDSFDIITCRYAAHHFSDVRKAVREVARVLKQDGRFLLVDHYAPEDPVLDEFVNHLNRLRDPSHVRESSLSEWQAmFSANQLAYQDIQKWNLPIQYDSWIKRGGTPADREKQIITHLNHASDEARDTFCITLNQNGQPISFCLKAILIQGIKREG 230
                                   | 6        16        26        36        46        56        66        76        86        96       106       116       126       136       146    |  156       166       176       186       196       206       216       226    
                                   4-MSE                                    46-MSE                                                                                                  151-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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (YCGJ_BACSU | O31474)
molecular function
    GO:0008757    S-adenosylmethionine-dependent methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        YCGJ_BACSU | O31474: 1xxl

(-) Related Entries Specified in the PDB File

1xxl RELATED ID: NYSGXRC-T1761 RELATED DB: TARGETDB