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(-) Description

Title :  STRUCTURE OF THE OBG GTP-BINDING PROTEIN
 
Authors :  J. Buglino, V. Shen, P. Hakimian, C. D. Lima, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  04 May 02  (Deposition) - 16 Sep 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Gtpase, Obg, Stringent Factor, Stress Response, Sporulation, Large G-Protein, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Buglino, V. Shen, P. Hakimian, C. D. Lima
Structural And Biochemical Analysis Of The Obg Gtp Binding Protein
Structure V. 10 1581 2002
PubMed-ID: 12429099  |  Reference-DOI: 10.1016/S0969-2126(02)00882-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SPO0B-ASSOCIATED GTP-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 1- 342 OF P20964
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Other Details: FULL-LENGTH PROTEIN, RESIDUES 1-428, WAS PURIFIED AND PREPARTIVELY PROTEOLYZED WITH SUBTILISIN TO OBTAIN THE 1-342 FRAGMENT
    Synonym: GTP-BINDING PROTEIN OBG

 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, 28)

Asymmetric Unit (3, 28)
No.NameCountTypeFull Name
1G4P1Ligand/IonGUANOSINE-5',3'-TETRAPHOSPHATE
2MG7Ligand/IonMAGNESIUM ION
3MSE20Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1G4P-1Ligand/IonGUANOSINE-5',3'-TETRAPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 11)
No.NameCountTypeFull Name
1G4P1Ligand/IonGUANOSINE-5',3'-TETRAPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:172 , G4P B:600BINDING SITE FOR RESIDUE MG B 901
2AC2SOFTWAREG4P B:600BINDING SITE FOR RESIDUE MG B 902
3AC3SOFTWAREASN B:142 , HOH B:1019 , HOH B:1024 , HOH B:1077BINDING SITE FOR RESIDUE MG B 903
4AC4SOFTWAREGLN A:222 , GLY A:225 , LEU A:226 , GLY A:227 , HOH A:995 , HOH A:996 , HOH A:997BINDING SITE FOR RESIDUE MG A 904
5AC5SOFTWAREGLU A:144 , HOH B:1014BINDING SITE FOR RESIDUE MG B 905
6AC6SOFTWAREASP A:203BINDING SITE FOR RESIDUE MG A 906
7AC7SOFTWAREASN B:17BINDING SITE FOR RESIDUE MG B 907
8AC8SOFTWARESER B:168 , VAL B:169 , GLY B:170 , LYS B:171 , SER B:172 , THR B:173 , ASN B:282 , LYS B:283 , ASP B:285 , SER B:310 , ALA B:311 , VAL B:312 , MG B:901 , MG B:902 , HOH B:918 , HOH B:943 , HOH B:1029BINDING SITE FOR RESIDUE G4P B 600

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_OBGPS51710 OBG-type guanine nucleotide-binding (G) domain profile.OBG_BACSU159-329
 		  2A:159-329
B:159-329
2GTP1_OBGPS00905 GTP1/OBG family signature.OBG_BACSU212-225
 		  2A:212-225
B:212-218
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_OBGPS51710 OBG-type guanine nucleotide-binding (G) domain profile.OBG_BACSU159-329
 		  1A:159-329
-
2GTP1_OBGPS00905 GTP1/OBG family signature.OBG_BACSU212-225
 		  1A:212-225
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_OBGPS51710 OBG-type guanine nucleotide-binding (G) domain profile.OBG_BACSU159-329
 		  1-
B:159-329
2GTP1_OBGPS00905 GTP1/OBG family signature.OBG_BACSU212-225
 		  1-
B:212-218

(-) Exons   (0, 0)

(no "Exon" information available for 1LNZ)

(-) 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:342
 aligned with OBG_BACSU | P20964 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:342
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340  
            OBG_BACSU     1 MFVDQVKVYVKGGDGGNGMVAFRREKYVPKGGPAGGDGGKGGDVVFEVDEGLRTLMDFRYKKHFKAIRGEHGMSKNQHGRNADDMVIKVPPGTVVTDDDTKQVIADLTEHGQRAVIARGGRGGRGNSRFATPANPAPQLSENGEPGKERYIVLELKVLADVGLVGFPSVGKSTLLSVVSSAKPKIADYHFTTLVPNLGMVETDDGRSFVMADLPGLIEGAHQGVGLGHQFLRHIERTRVIVHVIDMSGLEGRDPYDDYLTINQELSEYNLRLTERPQIIVANKMDMPEAAENLEAFKEKLTDDYPVFPISAVTREGLRELLFEVANQLENTPEFPLYDEEEL 342
               SCOP domains d1lnza1 A:1-157 Obg GTP-binding protein N-terminal domain                                                                                                    d1lnza2 A:158-342 Obg GTP-binding protein middle domain                                                                                                                                   SCOP domains
               CATH domains -1lnzA01 A:2-157  [code=2.70.210.12, no name defined]                                                                                                        1lnzA02 A:158-342 P-loop containing nucleotide triphosphate hydrolases                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeee................................eeeee.......hhhhh..eee...................eeeee...eeeee.....eeeee.....eeeee.......hhhhh..................eeeeeeeee....eeee.....hhhhhhhhheee..ee...........eeeee.....eeeeeehhhhhhhh.....hhhhhhhhhhhh.eeeeeee.......hhhhhhhhhhhhhhhh...........eee.....hhhhhhhhhhhhh................hhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------G_OBG  PDB: A:159-329 UniProt: 159-329                                                                                                                                     ------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTP1_OBG      --------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1lnz A   1 mFVDQVKVYVKGGDGGNGmVAFRREKYVPKGGPAGGDGGKGGDVVFEVDEGLRTLmDFRYKKHFKAIRGEHGmSKNQHGRNADDmVIKVPPGTVVTDDDTKQVIADLTEHGQRAVIARGGRGGRGNSRFATPANPAPQLSENGEPGKERYIVLELKVLADVGLVGFPSVGKSTLLSVVSSAKPKIADYHFTTLVPNLGmVETDDGRSFVmADLPGLIEGAHQGVGLGHQFLRHIERTRVIVHVIDmSGLEGRDPYDDYLTINQELSEYNLRLTERPQIIVANKmDmPEAAENLEAFKEKLTDDYPVFPISAVTREGLRELLFEVANQLENTPEFPLYDEEEL 342
                            |       10        20        30        40        50     |  60        70  |     80    |   90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     | 250       260       270       280   | | 290       300       310       320       330       340  
                            |                19-MSE                               56-MSE           73-MSE      85-MSE                                                                                                           199-MSE    210-MSE                             246-MSE                               284-MSE                                                      
                            1-MSE                                                                                                                                                                                                                                                                                      286-MSE                                                    


Chain B from PDB  Type:PROTEIN  Length:320
 aligned with OBG_BACSU | P20964 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:337
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       
            OBG_BACSU     1 MFVDQVKVYVKGGDGGNGMVAFRREKYVPKGGPAGGDGGKGGDVVFEVDEGLRTLMDFRYKKHFKAIRGEHGMSKNQHGRNADDMVIKVPPGTVVTDDDTKQVIADLTEHGQRAVIARGGRGGRGNSRFATPANPAPQLSENGEPGKERYIVLELKVLADVGLVGFPSVGKSTLLSVVSSAKPKIADYHFTTLVPNLGMVETDDGRSFVMADLPGLIEGAHQGVGLGHQFLRHIERTRVIVHVIDMSGLEGRDPYDDYLTINQELSEYNLRLTERPQIIVANKMDMPEAAENLEAFKEKLTDDYPVFPISAVTREGLRELLFEVANQLENTPEFPLY 337
               SCOP domains d1lnzb1 B:1-157 Obg GTP-binding protein N-terminal domain                                                                                                    d1lnzb2 B:158-337 Obg GTP-bi         nding protein middle dom        ain                                                                                                             SCOP domains
               CATH domains -1lnzB01 B:2-157  [code=2.70.210.12, no name defined]                                                                                                        1lnzB02 B:158-337 P-loop con         taining nucleotide triph        osphate hydrolases                                                                                              CATH domains
           Pfam domains (1) -GTP1_OBG-1lnzB03 B:2-157                                                                                                                                    --MMR_HSR1-1lnzB01 B:160-283                                                                                                  ------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) -GTP1_OBG-1lnzB04 B:2-157                                                                                                                                    --MMR_HSR1-1lnzB02 B:160-283                                                                                                  ------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ..eeeeeeeee..........eeee..eeeeee..........eeeee......hhhhhh..eee...................eeeee...eeeee.....eeeee.....eeeee.......hhhhhh.................eeeeeeeee....eeee.....hhhhhhhhh.......---------..eeeee.....eeeeeehhhhhh--------.hhhhhhhhhh.eeeeeee.......hhhhhhhhhhhhhhh.........eeeeee.....hhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------G_OBG  PDB: B:159-329 UniProt: 159-329                                                                                                                                     -------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTP1_OBG      ---------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lnz B   1 mFVDQVKVYVKGGDGGNGmVAFRREKYVPKGGPAGGDGGKGGDVVFEVDEGLRTLmDFRYKKHFKAIRGEHGmSKNQHGRNADDmVIKVPPGTVVTDDDTKQVIADLTEHGQRAVIARGGRGGRGNSRFATPANPAPQLSENGEPGKERYIVLELKVLADVGLVGFPSVGKSTLLSVVSSAKPKI---------PNLGmVETDDGRSFVmADLPGLIE--------GHQFLRHIERTRVIVHVIDmSGLEGRDPYDDYLTINQELSEYNLRLTERPQIIVANKmDmPEAAENLEAFKEKLTDDYPVFPISAVTREGLRELLFEVANQLENTPEFPLY 337
                            |       10        20        30        40        50     |  60        70  |     80    |   90       100       110       120       130       140       150       160       170       180    |    -    |  200       210       | -      |230       240     | 250       260       270       280   | | 290       300       310       320       330       
                            1-MSE            19-MSE                               56-MSE           73-MSE      85-MSE                                                                                             185       195   |        210-MSE 218      227                246-MSE                               284-MSE                                                 
                                                                                                                                                                                                                                199-MSE                                                                                286-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  (2, 4)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Clan: no clan defined [family: GTP1_OBG] (2)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (OBG_BACSU | P20964)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
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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