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(-) Description

Title :  CRYSTAL STRUCTURE OF A METHYLTRANSFERASE-LIKE PROTEIN (SPO2022) FROM SILICIBACTER POMEROYI DSS-3 AT 1.80 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  18 Apr 08  (Deposition) - 06 May 08  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Rossmann Fold, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Methyltransferase-Like Protein Of Unknown Function (Yp_167254. 1) From Silicibacter Pomeroyi Dss-3 At 1. 80 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METHYLTRANSFERASE-LIKE PROTEIN OF UNKNOWN FUNCTION
    Atcc: 700808
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YP_167254.1, SPO2022
    Organism Scientific: SILICIBACTER POMEROYI DSS-3
    Organism Taxid: 246200
    Strain: DSS-3 / DSM 15171

 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  (5, 82)

Asymmetric Unit (5, 82)
No.NameCountTypeFull Name
1EDO46Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3MSE32Mod. Amino AcidSELENOMETHIONINE
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 43)
No.NameCountTypeFull Name
1EDO25Ligand/Ion1,2-ETHANEDIOL
2GOL-1Ligand/IonGLYCEROL
3MSE16Mod. Amino AcidSELENOMETHIONINE
4PG4-1Ligand/IonTETRAETHYLENE GLYCOL
5SO42Ligand/IonSULFATE ION
Biological Unit 2 (4, 39)
No.NameCountTypeFull Name
1EDO21Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3MSE16Mod. Amino AcidSELENOMETHIONINE
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5SO4-1Ligand/IonSULFATE ION

(-) Sites  (50, 50)

Asymmetric Unit (50, 50)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:60 , ALA A:61 , ARG A:64BINDING SITE FOR RESIDUE SO4 A 202
02AC2SOFTWAREARG B:120 , HIS B:121 , ARG B:158 , TRP B:159BINDING SITE FOR RESIDUE SO4 B 202
03AC3SOFTWAREALA D:46 , GLU D:47 , TRP D:69 , ASN D:73 , PRO D:74BINDING SITE FOR RESIDUE EDO D 202
04AC4SOFTWAREPRO A:90 , SER A:99 , ALA A:101 , GLU D:21 , ARG D:24BINDING SITE FOR RESIDUE EDO A 203
05AC5SOFTWAREARG B:10 , PRO B:11 , GLU B:12 , GLY B:40BINDING SITE FOR RESIDUE EDO B 203
06AC6SOFTWAREALA A:101 , ARG A:104 , ASP B:100 , PRO D:17 , ALA D:18 , GLU D:21BINDING SITE FOR RESIDUE EDO A 204
07AC7SOFTWAREHIS B:96 , PRO B:146 , PRO B:201BINDING SITE FOR RESIDUE EDO B 204
08AC8SOFTWARETHR B:148 , PHE B:179 , GLN B:180BINDING SITE FOR RESIDUE EDO D 203
09AC9SOFTWARELYS C:102 , SER C:105BINDING SITE FOR RESIDUE EDO C 202
10BC1SOFTWAREARG A:104 , ARG B:196 , THR B:199 , SER B:200BINDING SITE FOR RESIDUE EDO B 205
11BC2SOFTWARETHR A:54 , PHE A:119 , ARG A:120BINDING SITE FOR RESIDUE EDO A 205
12BC3SOFTWARETHR D:54 , PHE D:119 , ARG D:120BINDING SITE FOR RESIDUE EDO D 204
13BC4SOFTWAREARG A:60 , ARG A:64BINDING SITE FOR RESIDUE EDO A 206
14BC5SOFTWAREARG D:10 , PRO D:11 , GLY D:40BINDING SITE FOR RESIDUE EDO D 205
15BC6SOFTWAREARG A:120 , HIS A:121BINDING SITE FOR RESIDUE EDO A 207
16BC7SOFTWARESER C:99 , ASP C:100BINDING SITE FOR RESIDUE EDO C 203
17BC8SOFTWAREPRO C:188 , SER D:142 , THR D:144BINDING SITE FOR RESIDUE EDO D 206
18BC9SOFTWARETHR C:54 , THR C:116 , PHE C:119 , ARG C:120BINDING SITE FOR RESIDUE EDO C 204
19CC1SOFTWAREHIS B:52 , THR B:54 , ASN B:82 , GLU B:117 , GLY B:118BINDING SITE FOR RESIDUE EDO B 206
20CC2SOFTWARELEU D:70 , PRO D:75 , GLU D:80BINDING SITE FOR RESIDUE EDO D 207
21CC3SOFTWAREGLU D:31 , GLY D:50 , LYS D:51 , HIS D:52 , GLY D:78 , ARG D:120BINDING SITE FOR RESIDUE EDO D 208
22CC4SOFTWAREARG A:104BINDING SITE FOR RESIDUE EDO A 208
23CC5SOFTWAREARG B:64 , LYS B:67BINDING SITE FOR RESIDUE EDO B 207
24CC6SOFTWAREARG B:64BINDING SITE FOR RESIDUE EDO B 208
25CC7SOFTWAREARG A:64 , LYS A:67 , TRP A:85BINDING SITE FOR RESIDUE EDO A 209
26CC8SOFTWARETRP A:85 , THR A:86 , ASP A:87BINDING SITE FOR RESIDUE EDO A 210
27CC9SOFTWAREARG D:60 , ARG D:64BINDING SITE FOR RESIDUE EDO D 209
28DC1SOFTWAREARG D:64 , LYS D:67BINDING SITE FOR RESIDUE EDO D 210
29DC2SOFTWAREARG C:60 , ARG C:64BINDING SITE FOR RESIDUE EDO C 205
30DC3SOFTWAREARG C:60 , ARG C:64 , LYS C:67 , TRP C:85BINDING SITE FOR RESIDUE EDO C 206
31DC4SOFTWAREARG A:196 , ARG B:115BINDING SITE FOR RESIDUE EDO A 211
32DC5SOFTWAREPHE D:166 , LEU D:167 , GLY D:168 , GLN D:180 , GLU D:182 , GLN D:184BINDING SITE FOR RESIDUE EDO D 211
33DC6SOFTWAREHIS A:52 , THR A:54 , ASN A:82 , GLY A:118BINDING SITE FOR RESIDUE EDO A 212
34DC7SOFTWARETRP D:114 , ARG D:115 , THR D:116 , PHE D:119BINDING SITE FOR RESIDUE EDO D 212
35DC8SOFTWARETRP B:85 , THR B:86 , ASP B:87BINDING SITE FOR RESIDUE EDO B 209
36DC9SOFTWARETRP B:85 , ALA B:112BINDING SITE FOR RESIDUE EDO B 210
37EC1SOFTWARESER A:99 , ALA D:20 , GLU D:21BINDING SITE FOR RESIDUE EDO D 213
38EC2SOFTWAREARG C:10 , PRO C:11 , LEU C:13BINDING SITE FOR RESIDUE EDO C 207
39EC3SOFTWAREHIS B:121 , ARG B:145 , ARG B:157 , TRP B:159BINDING SITE FOR RESIDUE EDO B 211
40EC4SOFTWAREASP B:59 , GLY B:95BINDING SITE FOR RESIDUE EDO B 212
41EC5SOFTWAREASP A:59BINDING SITE FOR RESIDUE EDO A 213
42EC6SOFTWARETHR B:54 , THR B:116 , PHE B:119 , ARG B:120BINDING SITE FOR RESIDUE EDO B 213
43EC7SOFTWAREARG C:60 , ARG C:64BINDING SITE FOR RESIDUE EDO C 208
44EC8SOFTWAREALA A:71 , ARG D:60 , ALA D:61 , ARG D:64BINDING SITE FOR RESIDUE EDO D 214
45EC9SOFTWAREARG B:60 , ARG B:64BINDING SITE FOR RESIDUE EDO B 214
46FC1SOFTWAREARG D:120 , HIS D:121BINDING SITE FOR RESIDUE EDO D 215
47FC2SOFTWAREARG A:10 , PRO A:11 , LEU A:13 , ARG A:24 , GLY A:40BINDING SITE FOR RESIDUE EDO A 214
48FC3SOFTWAREARG B:115 , ARG B:157 , ARG B:175BINDING SITE FOR RESIDUE EDO B 215
49FC4SOFTWAREGLU B:29 , ASP B:123 , THR B:148 , GLN B:180BINDING SITE FOR RESIDUE PG4 D 216
50FC5SOFTWARESER B:58 , ARG B:60 , TRP B:85 , GLY B:89 , PRO B:90 , THR B:91BINDING SITE FOR RESIDUE GOL C 209

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CVO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CVO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CVO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CVO)

(-) Exons   (0, 0)

(no "Exon" information available for 3CVO)

(-) 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:194
 aligned with Q5LRV1_RUEPO | Q5LRV1 from UniProtKB/TrEMBL  Length:201

    Alignment length:194
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197    
         Q5LRV1_RUEPO     8 QMRPELTMPPAEAEALRMAYEEAEVILEYGSGGSTVVAAELPGKHVTSVESDRAWARMMKAWLAANPPAEGTEVNIVWTDIGPTGDWGHPVSDAKWRSYPDYPLAVWRTEGFRHPDVVLVDGRFRVGCALATAFSITRPVTLLFDDYSQRRWQHQVEEFLGAPLMIGRLAAFQVEPQPIPPGSLMQLIRTMTSP 201
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cvoA00 A:8-201 Vaccinia Virus protein VP39                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh.eeeee..hhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh......eeeeee......hhhhh.....hhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhhhh...eeeee.hhhhh.hhhhhhhhhh..eee..eeeeee.....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cvo A   8 QmRPELTmPPAEAEALRmAYEEAEVILEYGSGGSTVVAAELPGKHVTSVESDRAWARmmKAWLAANPPAEGTEVNIVWTDIGPTGDWGHPVSDAKWRSYPDYPLAVWRTEGFRHPDVVLVDGRFRVGCALATAFSITRPVTLLFDDYSQRRWQHQVEEFLGAPLmIGRLAAFQVEPQPIPPGSLmQLIRTmTSP 201
                             |     |17       |27        37        47        57       |67        77        87        97       107       117       127       137       147       157       167    |  177       187    |  197|   
                             |     |        25-MSE                                  65-MSE                                                                                                    172-MSE             192-MSE |   
                             9-MSE |                                                 66-MSE                                                                                                                             198-MSE
                                  15-MSE                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:194
 aligned with Q5LRV1_RUEPO | Q5LRV1 from UniProtKB/TrEMBL  Length:201

    Alignment length:194
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197    
         Q5LRV1_RUEPO     8 QMRPELTMPPAEAEALRMAYEEAEVILEYGSGGSTVVAAELPGKHVTSVESDRAWARMMKAWLAANPPAEGTEVNIVWTDIGPTGDWGHPVSDAKWRSYPDYPLAVWRTEGFRHPDVVLVDGRFRVGCALATAFSITRPVTLLFDDYSQRRWQHQVEEFLGAPLMIGRLAAFQVEPQPIPPGSLMQLIRTMTSP 201
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cvoB00 B:8-201 Vaccinia Virus protein VP39                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh.eeeee..hhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh......eeeeee................hhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh..eee..eeeeee.....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cvo B   8 QmRPELTmPPAEAEALRmAYEEAEVILEYGSGGSTVVAAELPGKHVTSVESDRAWARmmKAWLAANPPAEGTEVNIVWTDIGPTGDWGHPVSDAKWRSYPDYPLAVWRTEGFRHPDVVLVDGRFRVGCALATAFSITRPVTLLFDDYSQRRWQHQVEEFLGAPLmIGRLAAFQVEPQPIPPGSLmQLIRTmTSP 201
                             |     |17       |27        37        47        57       |67        77        87        97       107       117       127       137       147       157       167    |  177       187    |  197|   
                             |     |        25-MSE                                  65-MSE                                                                                                    172-MSE             192-MSE |   
                             9-MSE |                                                 66-MSE                                                                                                                             198-MSE
                                  15-MSE                                                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:194
 aligned with Q5LRV1_RUEPO | Q5LRV1 from UniProtKB/TrEMBL  Length:201

    Alignment length:194
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197    
         Q5LRV1_RUEPO     8 QMRPELTMPPAEAEALRMAYEEAEVILEYGSGGSTVVAAELPGKHVTSVESDRAWARMMKAWLAANPPAEGTEVNIVWTDIGPTGDWGHPVSDAKWRSYPDYPLAVWRTEGFRHPDVVLVDGRFRVGCALATAFSITRPVTLLFDDYSQRRWQHQVEEFLGAPLMIGRLAAFQVEPQPIPPGSLMQLIRTMTSP 201
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cvoC00 C:8-201 Vaccinia Virus protein VP39                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh.eeeee..hhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh......eeeeee......hhhhh.....hhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh..eee..eeeeee.....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cvo C   8 QmRPELTmPPAEAEALRmAYEEAEVILEYGSGGSTVVAAELPGKHVTSVESDRAWARmmKAWLAANPPAEGTEVNIVWTDIGPTGDWGHPVSDAKWRSYPDYPLAVWRTEGFRHPDVVLVDGRFRVGCALATAFSITRPVTLLFDDYSQRRWQHQVEEFLGAPLmIGRLAAFQVEPQPIPPGSLmQLIRTmTSP 201
                             |     |17       |27        37        47        57       |67        77        87        97       107       117       127       137       147       157       167    |  177       187    |  197|   
                             |     |        25-MSE                                  65-MSE                                                                                                    172-MSE             192-MSE |   
                             9-MSE |                                                 66-MSE                                                                                                                             198-MSE
                                  15-MSE                                                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:194
 aligned with Q5LRV1_RUEPO | Q5LRV1 from UniProtKB/TrEMBL  Length:201

    Alignment length:194
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197    
         Q5LRV1_RUEPO     8 QMRPELTMPPAEAEALRMAYEEAEVILEYGSGGSTVVAAELPGKHVTSVESDRAWARMMKAWLAANPPAEGTEVNIVWTDIGPTGDWGHPVSDAKWRSYPDYPLAVWRTEGFRHPDVVLVDGRFRVGCALATAFSITRPVTLLFDDYSQRRWQHQVEEFLGAPLMIGRLAAFQVEPQPIPPGSLMQLIRTMTSP 201
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cvoD00 D:8-201 Vaccinia Virus protein VP39                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh.eeeee..hhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh......eeeeee......hhhhh.....hhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh..eee..eeeeee.....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cvo D   8 QmRPELTmPPAEAEALRmAYEEAEVILEYGSGGSTVVAAELPGKHVTSVESDRAWARmmKAWLAANPPAEGTEVNIVWTDIGPTGDWGHPVSDAKWRSYPDYPLAVWRTEGFRHPDVVLVDGRFRVGCALATAFSITRPVTLLFDDYSQRRWQHQVEEFLGAPLmIGRLAAFQVEPQPIPPGSLmQLIRTmTSP 201
                             |     |17       |27        37        47        57       |67        77        87        97       107       117       127       137       147       157       167    |  177       187    |  197|   
                             |     |        25-MSE                                  65-MSE                                                                                                    172-MSE             192-MSE |   
                             9-MSE |                                                 66-MSE                                                                                                                             198-MSE
                                  15-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 3CVO)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CVO)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q5LRV1_RUEPO | Q5LRV1)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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