1T9H - JenaLib

Title :   THE CRYSTAL STRUCTURE OF YLOQ, A CIRCULARLY PERMUTED GTPASE.

Authors :   V. M. Levdikov, E. V. Blagova, J. A. Brannigan, L. Cladiere, A. A. Antson, M. N. Isupov, S. J. Seror, A. J. Wilkinson

Date :   17 May 04 (Deposition) - 02 Nov 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A

Keywords :   N-Terminal Beta-Barrel Domain With Oligonucleotide Binding Fold, Central Gtp Binding Domain, C-Terminal Zinc-Binding Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. M. Levdikov, E. V. Blagova, J. A. Brannigan, L. Cladiere, A. A. Antson, M. N. Isupov, S. J. Seror, A. J. Wilkinson
The Crystal Structure Of Yloq, A Circularly Permuted Gtpase Essential For Bacillus Subtilis Viability.
J. Mol. Biol. V. 340 767 2004
PubMed-ID: 15223319 | Reference-DOI: 10.1016/J.JMB.2004.05.029
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 16)

Sites (16, 16)

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:-2 , HIS A:-4 , HIS A:-3 , HIS A:-1 , ASN A:54 , IUM A:407 , ACT A:417 , HOH A:424 , HOH A:436 , HOH A:479	BINDING SITE FOR RESIDUE IUM A 401
02	AC2	SOFTWARE	HIS A:-4 , GLU A:105 , PRO A:111 , PRO A:243 , ARG A:246 , IUM A:408 , ACT A:416 , HOH A:419 , HOH A:420 , HOH A:465	BINDING SITE FOR RESIDUE IUM A 402
03	AC3	SOFTWARE	ARG A:246 , IUM A:404 , IUM A:406 , IUM A:408 , ACT A:416 , ACT A:418 , HOH A:419 , HOH A:422 , HOH A:440 , HOH A:463	BINDING SITE FOR RESIDUE IUM A 403
04	AC4	SOFTWARE	ARG A:30 , GLU A:57 , IUM A:403 , ACT A:418 , HOH A:422 , HOH A:425 , HOH A:458	BINDING SITE FOR RESIDUE IUM A 404
05	AC5	SOFTWARE	GLU A:53 , LYS A:56 , GLU A:57 , TYR A:59 , HOH A:425	BINDING SITE FOR RESIDUE IUM A 405
06	AC6	SOFTWARE	HIS A:-1 , GLU A:53 , LYS A:56 , IUM A:403 , IUM A:408 , ACT A:417 , HOH A:422 , HOH A:425 , HOH A:440 , HOH A:458 , HOH A:587	BINDING SITE FOR RESIDUE IUM A 406
07	AC7	SOFTWARE	ARG A:-6 , HIS A:-5 , HIS A:-4 , HIS A:-3 , ASN A:54 , ASP A:108 , IUM A:401 , HOH A:436 , HOH A:451 , HOH A:453 , HOH A:607	BINDING SITE FOR RESIDUE IUM A 407
08	AC8	SOFTWARE	HIS A:-4 , HIS A:-1 , ARG A:246 , IUM A:402 , IUM A:403 , IUM A:406 , ACT A:417 , HOH A:419 , HOH A:420 , HOH A:424 , HOH A:440 , HOH A:465	BINDING SITE FOR RESIDUE IUM A 408
09	AC9	SOFTWARE	CYS A:252 , CYS A:257 , HIS A:259 , CYS A:265	BINDING SITE FOR RESIDUE ZN A 411
10	BC1	SOFTWARE	ASP A:143 , TYR A:145 , HOH A:549	BINDING SITE FOR RESIDUE CA A 412
11	BC2	SOFTWARE	HIS A:-1 , GLU A:247	BINDING SITE FOR RESIDUE CA A 413
12	BC3	SOFTWARE	GLU A:210 , HOH A:658 , HOH A:663	BINDING SITE FOR RESIDUE CA A 414
13	BC4	SOFTWARE	GLU A:286 , HOH A:521 , HOH A:595	BINDING SITE FOR RESIDUE CA A 415
14	BC5	SOFTWARE	GLU A:105 , GLY A:141 , TYR A:142 , PRO A:243 , IUM A:402 , IUM A:403 , ACT A:418 , HOH A:419	BINDING SITE FOR RESIDUE ACT A 416
15	BC6	SOFTWARE	HIS A:-2 , GLU A:53 , ASN A:54 , IUM A:401 , IUM A:406 , IUM A:408 , HOH A:424 , HOH A:440 , HOH A:587	BINDING SITE FOR RESIDUE ACT A 417
16	BC7	SOFTWARE	PHE A:13 , GLU A:57 , GLY A:141 , IUM A:403 , IUM A:404 , ACT A:416 , HOH A:422	BINDING SITE FOR RESIDUE ACT A 418

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:287
 aligned with RSGA_BACSU | O34530 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:306
                                    1                                                                                                                                                                                                                                                                                                         
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292      
           RSGA_BACSU     - --------MPEGKIIKALSGFYYVLDESEDSDKVIQCRGRGIFRKNKITPLVGDYVVYQAENDKEGYLMEIKERTNELIRPPICNVDQAVLVFSAVQPSFSTALLDRFLVLVEANDIQPIICITKMDLIEDQDTEDTIQAYAEDYRNIGYDVYLTSSKDQDSLADIIPHFQDKTTVFAGQSGVGKSSLLNAISPELGLRTNEISEHLGRGKHTTRHVELIHTSGGLVADTPGFSSLEFTDIEEEELGYTFPDIREKSSSCKFRGCLHLKEPKCAVKQAVEDGELKQYRYDHYVEFMTEIKDRKPRY 298
               SCOP domains --------d1t9ha1 A:1-67 Probable GTPase EngC (YjeQ), N-terminal domain      d1t9ha2 A:68-298 Probable GTPase EngC (YjeQ), C-terminal domain                                                                                                                                                                         SCOP domains
               CATH domains 1t9hA01 A:-7-65 Nucleic acid-binding proteins                            1t9hA02 A:66-230 P-loop containing nucleotide triphosphate hydrolases                                                                                                1t9hA03 A:231-298 Probable gtpase engc; domain 3                     CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------------------------DUF258-1t9hA01 A:130-289                                                                                                                                        --------- Pfam domains
         Sec.struct. author ..........eeeeeeee..eeeeee......eeeeee................eeeee......eeeeee.....ee....ee...eeeeeee......hhhhhhhhhhhhhh...eeeeeeehhhhh.hhhhhhhhhhhhhhhhhhh..eee.hhhhhh....hhhhhh..eeeeeehhhhhhhhhhhhhh.-------------------.....eeee..eeee.............hhhhhh..hhhhhhhhhhh............hhhhhhhhh...hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------G_CP  PDB: A:67-228 UniProt: 67-228                                                                                                                               ---------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------ENGC_GTPASE  PDB: A:76-226 UniProt: 76-226                                                                                                             ------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1t9h A  -7 ARHHHHHHMPEGKIIKALSGFYYVLDESEDSDKVIQCRGRGIFRKNKITPLVGDYVVYQAENDKEGYLMEIKERTNELIRPPICNVDQAVLVFSAVQPSFSTALLDRFLVLVEANDIQPIICITKMDLIEDQDTEDTIQAYAEDYRNIGYDVYLTSSKDQDSLADIIPHFQDKTTVFAGQSGVGKSSLLNAISP-------------------TRHVELIHTSGGLVADTPGFSSLEFTDIEEEELGYTFPDIREKSSSCKFRGCLHLKEPKCAVKQAVEDGELKQYRYDHYVEFMTEIKDRKPRY 298
                                     2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182   |     -         -   |   212       222       232       242       252       262       272       282       292      
                                                                                                                                                                                                                           186                 206

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (3, 3)

Pfam Domains (1, 1)

Gene Ontology (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RSGA_BACSU | O34530)


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: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.

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	Cis Peptide Bonds
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