1U0L - JenaLib

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Title :   CRYSTAL STRUCTURE OF YJEQ FROM THERMOTOGA MARITIMA

Authors :   D. H. Shin, Y. Lou, J. Jaru, R. Kim, H. Yokota, S. H. Kim, Berkeley Structural Genomics Center (Bsgc)

Date :   13 Jul 04 (Deposition) - 07 Sep 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Gtpase, Permutation, Ob-Fold, Zinc-Finger, Structural Genomics, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. H. Shin, Y. Lou, J. Jancarik, H. Yokota, R. Kim, S. H. Kim
Crystal Structure Of Yjeq From Thermotoga Maritima Contains A Circularly Permuted Gtpase Domain
Proc. Natl. Acad. Sci. Usa V. 101 13198 2004
PubMed-ID: 15331784 | Reference-DOI: 10.1073/PNAS.0405202101
(for further references see the PDB file header)

Molecule 1 - PROBABLE GTPASE ENGC
	Chains	:	A, B, C
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	BL21(DE3)
	Expression System Plasmid	:	PSJS1244
	Expression System Taxid	:	562
	Expression System Vector	:	PB4 (HOME MADE VECTOR)
	Expression System Vector Type	:	PLASMID
	Gene	:	ENGC, YJEQ
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	GDP	3	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:250 , CYS A:255 , HIS A:257 , CYS A:263	BINDING SITE FOR RESIDUE ZN A 298
2	AC2	SOFTWARE	CYS B:550 , CYS B:555 , HIS B:557 , CYS B:563	BINDING SITE FOR RESIDUE ZN B 598
3	AC3	SOFTWARE	CYS C:850 , CYS C:855 , HIS C:857 , CYS C:863	BINDING SITE FOR RESIDUE ZN C 898
4	AC4	SOFTWARE	ASN A:117 , LYS A:118 , ASP A:120 , LEU A:121 , SER A:147 , ALA A:148 , LYS A:149 , GLY A:173 , VAL A:174 , GLY A:175 , LYS A:176 , SER A:177 , SER A:178 , LEU A:189	BINDING SITE FOR RESIDUE GDP A 299
5	AC5	SOFTWARE	ASN B:417 , LYS B:418 , ASP B:420 , LEU B:421 , SER B:447 , ALA B:448 , LYS B:449 , GLY B:473 , VAL B:474 , GLY B:475 , LYS B:476 , SER B:477 , SER B:478	BINDING SITE FOR RESIDUE GDP B 599
6	AC6	SOFTWARE	VAL A:269 , GLU A:270 , ASN A:271 , ASN C:717 , LYS C:718 , ASP C:720 , LEU C:721 , SER C:747 , ALA C:748 , SER C:772 , GLY C:773 , VAL C:774 , GLY C:775 , LYS C:776 , SER C:777 , SER C:778	BINDING SITE FOR RESIDUE GDP C 899

(no "SS Bond" information available for 1U0L)

(no "Cis Peptide Bond" information available for 1U0L)

(no "SAP(SNP)/Variant" information available for 1U0L)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_CP	PS51721	Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile.	RSGA_THEMA	68-228	3	A:68-228 B:368-528 C:668-828
2	ENGC_GTPASE	PS50936	EngC GTPase domain profile.	RSGA_THEMA	77-226	3	A:77-226 B:377-526 C:677-826

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_CP	PS51721	Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile.	RSGA_THEMA	68-228	1	A:68-228 - -
2	ENGC_GTPASE	PS50936	EngC GTPase domain profile.	RSGA_THEMA	77-226	1	A:77-226 - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_CP	PS51721	Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile.	RSGA_THEMA	68-228	1	- B:368-528 -
2	ENGC_GTPASE	PS50936	EngC GTPase domain profile.	RSGA_THEMA	77-226	1	- B:377-526 -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_CP	PS51721	Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile.	RSGA_THEMA	68-228	1	- - C:668-828
2	ENGC_GTPASE	PS50936	EngC GTPase domain profile.	RSGA_THEMA	77-226	1	- - C:677-826

(no "Exon" information available for 1U0L)

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:278
 aligned with RSGA_THEMA | Q9X242 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:291
                                    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_THEMA     3 LRRRGIVVSFHSNMVTVEDEETGERILCKLRGKFRLQNLKIYVGDRVEYTPDETGSGVIENVLHRKNLLTKPHVANVDQVILVVTVKMPETSTYIIDKFLVLAEKNELETVMVINKMDLYDEDDLRKVRELEEIYSGLYPIVKTSAKTGMGIEELKEYLKGKISTMAGLSGVGKSSLLNAINPGLKLRVSEVSEKLQRGRHTTTTAQLLKFDFGGYVVDTPGFANLEINDIEPEELKHYFKEFGDKQCFFSDCNHVDEPECGVKEAVENGEIAESRYENYVKMFYELLGRR 293
               SCOP domains d1u0la1 A:3-68 Probable GTPase EngC (YjeQ), N-terminal domain     d1u0la2 A:69-293 Probable GTPase EngC (YjeQ), C-terminal domain                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------1u0lA02 A:67-230 P-loop containing nucleotide triphosphate hydrolases                                                                                               1u0lA03 A:231-293 Probable gtpase engc; domain 3                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee..eeeeee.....eeeeee.hhhh..........eeeee......eeeeee.....ee....ee...eeeeee.......hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhh....eee.......hhhhhhhhhh..eeeee.....hhhhhhhhhh......-------------......eee.....eee.............hhhhhhhhh....................hhhhhhhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------G_CP  PDB: A:68-228 UniProt: 68-228                                                                                                                              ----------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------ENGC_GTPASE  PDB: A:77-226 UniProt: 77-226                                                                                                            ------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u0l A   3 LRRRGIVVSFHSNMVTVEDEETGERILCKLRGKFRLQNLKIYVGDRVEYTPDETGSGVIENVLHRKNLLTKPHVANVDQVILVVTVKMPETSTYIIDKFLVLAEKNELETVMVINKMDLYDEDDLRKVRELEEIYSGLYPIVKTSAKTGMGIEELKEYLKGKISTMAGLSGVGKSSLLNAINPGLKLR-------------TTTTAQLLKFDFGGYVVDTPGFANLEINDIEPEELKHYFKEFGDKQCFFSDCNHVDEPECGVKEAVENGEIAESRYENYVKMFYELLGRR 293
                                    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 
                                                                                                                                                                                                                     190           204

Chain B from PDB  Type:PROTEIN  Length:278
 aligned with RSGA_THEMA | Q9X242 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:291
                                    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_THEMA     3 LRRRGIVVSFHSNMVTVEDEETGERILCKLRGKFRLQNLKIYVGDRVEYTPDETGSGVIENVLHRKNLLTKPHVANVDQVILVVTVKMPETSTYIIDKFLVLAEKNELETVMVINKMDLYDEDDLRKVRELEEIYSGLYPIVKTSAKTGMGIEELKEYLKGKISTMAGLSGVGKSSLLNAINPGLKLRVSEVSEKLQRGRHTTTTAQLLKFDFGGYVVDTPGFANLEINDIEPEELKHYFKEFGDKQCFFSDCNHVDEPECGVKEAVENGEIAESRYENYVKMFYELLGRR 293
               SCOP domains d1u0lb1 B:303-368 Probable GTPase EngC (YjeQ), N-terminal domain  d1u0lb2 B:369-593 Probable GTPase EngC (YjeQ), C-terminal domain                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------1u0lB02 B:367-530 P-loop containing nucleotide triphosphate hydrolases                                                                                              1u0lB03 B:531-593 Probable gtpase engc; domain 3                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee..eeeeee.....eeee.................eeeee.......eeeee.....ee....ee...eeeeee.......hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhh....eee.......hhhhhhhhhh..eeeee.....hhhhhhhh........-------------......eee.....eee.............hhhhhhhhh....................hhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------G_CP  PDB: B:368-528 UniProt: 68-228                                                                                                                             ----------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------ENGC_GTPASE  PDB: B:377-526 UniProt: 77-226                                                                                                           ------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u0l B 303 LRRRGIVVSFHSNMVTVEDEETGERILCKLRGKFRLQNLKIYVGDRVEYTPDETGSGVIENVLHRKNLLTKPHVANVDQVILVVTVKMPETSTYIIDKFLVLAEKNELETVMVINKMDLYDEDDLRKVRELEEIYSGLYPIVKTSAKTGMGIEELKEYLKGKISTMAGLSGVGKSSLLNAINPGLKLR-------------TTTTAQLLKFDFGGYVVDTPGFANLEINDIEPEELKHYFKEFGDKQCFFSDCNHVDEPECGVKEAVENGEIAESRYENYVKMFYELLGRR 593
                                   312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       | -         - |     512       522       532       542       552       562       572       582       592 
                                                                                                                                                                                                                     490           504

Chain C from PDB  Type:PROTEIN  Length:278
 aligned with RSGA_THEMA | Q9X242 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:291
                                    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_THEMA     3 LRRRGIVVSFHSNMVTVEDEETGERILCKLRGKFRLQNLKIYVGDRVEYTPDETGSGVIENVLHRKNLLTKPHVANVDQVILVVTVKMPETSTYIIDKFLVLAEKNELETVMVINKMDLYDEDDLRKVRELEEIYSGLYPIVKTSAKTGMGIEELKEYLKGKISTMAGLSGVGKSSLLNAINPGLKLRVSEVSEKLQRGRHTTTTAQLLKFDFGGYVVDTPGFANLEINDIEPEELKHYFKEFGDKQCFFSDCNHVDEPECGVKEAVENGEIAESRYENYVKMFYELLGRR 293
               SCOP domains d1u0lc1 C:603-668 Probable GTPase EngC (YjeQ), N-terminal domain  d1u0lc2 C:669-893 Probable GTPase EngC (YjeQ), C-terminal domain                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------1u0lC02 C:667-830 P-loop containing nucleotide triphosphate hydrolases                                                                                              1u0lC03 C:831-893 Probable gtpase engc; domain 3                CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------DUF258-1u0lC01 C:730-887                                                                                                                                      ------ Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------DUF258-1u0lC02 C:730-887                                                                                                                                      ------ Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------DUF258-1u0lC03 C:730-887                                                                                                                                      ------ Pfam domains (3)
         Sec.struct. author ..eeeeeeeee..eeeeee.....eee..................eeee..hhhhh....ee.....ee....ee...eeeeee.......hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhh....eee.......hhhhhhhhhh..eeeee.....hhhhhhhhhh......-------------......eee.....eee.............hhhhhhhhh....................hhhhhhhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------G_CP  PDB: C:668-828 UniProt: 68-228                                                                                                                             ----------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------ENGC_GTPASE  PDB: C:677-826 UniProt: 77-226                                                                                                           ------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u0l C 603 LRRRGIVVSFHSNMVTVEDEETGERILCKLRGKFRLQNLKIYVGDRVEYTPDETGSGVIENVLHRKNLLTKPHVANVDQVILVVTVKMPETSTYIIDKFLVLAEKNELETVMVINKMDLYDEDDLRKVRELEEIYSGLYPIVKTSAKTGMGIEELKEYLKGKISTMAGLSGVGKSSLLNAINPGLKLR-------------TTTTAQLLKFDFGGYVVDTPGFANLEINDIEPEELKHYFKEFGDKQCFFSDCNHVDEPECGVKEAVENGEIAESRYENYVKMFYELLGRR 893
                                   612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       | -         - |     812       822       832       842       852       862       872       882       892 
                                                                                                                                                                                                                     790           804

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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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Thermotoga maritima. Organism_taxid: 2336. (16)

1a	1u0lA02	A:67-230
1b	1u0lC02	C:667-830
1c	1u0lB02	B:367-530

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Ribonucleotide Reductase Protein R1; domain 1 (62)

Homologous Superfamily: Probable gtpase engc; domain 3 (3)

Thermotoga maritima. Organism_taxid: 2336. (1)

2a	1u0lA03	A:231-293
2b	1u0lB03	B:531-593
2c	1u0lC03	C:831-893

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: DUF258 (4)

Thermotoga maritima (1)

1a	DUF258-1u0lC01	C:730-887
1b	DUF258-1u0lC02	C:730-887
1c	DUF258-1u0lC03	C:730-887

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (RSGA_THEMA | Q9X242)


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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