1R8G - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE AND FUNCTION OF YBDK

Authors :   C. Lehmann, V. Doseeva, S. Pullalarevu, W. Krajewski, A. Howard, O. Herzberg, Structure 2 Function Project (S2F)

Date :   24 Oct 03 (Deposition) - 17 Aug 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym./Biol. Unit : A,B

Keywords :   Structural Genomics, Unknown Function, Ybdk, Hypothetical Protein, Carboxylate-Amine Ligase, Structure 2 Function Project, S2F (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Lehmann, V. Doseeva, S. Pullalarevu, W. Krajewski, A. Howard, O. Herzberg
Ybdk Is A Carboxylate-Amine Ligase With A Gamma-Glutamyl:Cysteine Ligase Activity: Crystal Structure And Enzymatic Assays
Proteins: V. 56 376 2004 Struct. , Funct. , Genet.
PubMed-ID: 15211520 | Reference-DOI: 10.1002/PROT.20103
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL PROTEIN YBDK
	Chains	:	A, B
	EC Number	:	6.3.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET100-D-TOPO
	Expression System Strain	:	BL21STAR(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YBDK, B0581
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 20)

No.	Name	Count	Type	Full Name
1	MSE	20	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1R8G)

(no "SS Bond" information available for 1R8G)

Asymmetric/Biological Unit

No.	Residues
1	Pro A:25	-	Pro A:26
2	Pro B:25	-	Pro B:26

(no "SAP(SNP)/Variant" information available for 1R8G)

(no "PROSITE Motif" information available for 1R8G)

(no "Exon" information available for 1R8G)

Asymmetric/Biological 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:352
 aligned with GCS2_ECOLI | P77213 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:368
                                    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       302       312       322       332       342       352       362        
           GCS2_ECOLI     3 LPDFHVSEPFTLGIELEMQVVNPPGYDLSQDSSMLIDAVKNKITAGEVKHDITESMLELATDVCRDINQAAGQFSAMQKVVLQAATDHHLEICGGGTHPFQKWQRQEVCDNERYQRTLENFGYLIQQATVFGQHVHVGCASGDDAIYLLHGLSRFVPHFIALSAASPYMQGTDTRFASSRPNIFSAFPDNGPMPWVSNWQQFEALFRCLSYTTMIDSIKDLHWDIRPSPHFGTVEVRVMDTPLTLSHAVNMAGLIQATAHWLLTERPFKHQEKDYLLYKFNRFQACRYGLEGVITDPHTGDRRPLTEDTLRLLEKIAPSAHKIGASSAIEALHRQVVSGLNEAQLMRDFVADGGSLIGLVKKHCEIWA 370
               SCOP domains d1r8ga_ A: Carboxylate-amine ligase YbdK                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeee....ee...hhhhhh.........eeee.....eeeee.....hhhhhhhhhhhhhhhhhhhhhhh..eee..........----------------.hhhhhh.....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.....hhhhhhh............hhhhhhhhhhhhh......hhhhh...eeee....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...eee......eeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r8g A   3 LPDFHVSEPFTLGIELEmQVVNPPGYDLSQDSSmLIDAVKNKITAGEVKHDITESmLELATDVCRDINQAAGQFSAmQKVVLQAATDHHLEICGGGTHPFQKW----------------NFGYLIQQATVFGQHVHVGCASGDDAIYLLHGLSRFVPHFIALSAASPYmQGTDTRFASSRPNIFSAFPDNGPmPWVSNWQQFEALFRCLSYTTmIDSIKDLHWDIRPSPHFGTVEVRVmDTPLTLSHAVNmAGLIQATAHWLLTERPFKHQEKDYLLYKFNRFQACRYGLEGVITDPHTGDRRPLTEDTLRLLEKIAPSAHKIGASSAIEALHRQVVSGLNEAQLmRDFVADGGSLIGLVKKHCEIWA 370
                                    12       |22        32   |    42        52     |  62        72      | 82        92       102  |      -       122       132       142       152       162       172       182       192  |    202       212   |   222       232       242       252|      262       272       282       292       302       312       322       332       342     | 352       362        
                                            20-MSE          36-MSE                58-MSE               79-MSE                   105              122                                              171-MSE                 195-MSE              216-MSE                  241-MSE     253-MSE                                                                                        348-MSE

Chain B from PDB  Type:PROTEIN  Length:358
 aligned with GCS2_ECOLI | P77213 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:369
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361         
           GCS2_ECOLI     2 PLPDFHVSEPFTLGIELEMQVVNPPGYDLSQDSSMLIDAVKNKITAGEVKHDITESMLELATDVCRDINQAAGQFSAMQKVVLQAATDHHLEICGGGTHPFQKWQRQEVCDNERYQRTLENFGYLIQQATVFGQHVHVGCASGDDAIYLLHGLSRFVPHFIALSAASPYMQGTDTRFASSRPNIFSAFPDNGPMPWVSNWQQFEALFRCLSYTTMIDSIKDLHWDIRPSPHFGTVEVRVMDTPLTLSHAVNMAGLIQATAHWLLTERPFKHQEKDYLLYKFNRFQACRYGLEGVITDPHTGDRRPLTEDTLRLLEKIAPSAHKIGASSAIEALHRQVVSGLNEAQLMRDFVADGGSLIGLVKKHCEIWA 370
               SCOP domains d1r8gb_ B: Carboxylate-amine ligase YbdK                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeeee....ee..hhhhhhhhhh......eee.-....eeeee.....hhhhhhhhhhhhhhhhhhhhhhh..eee...........----------.hhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.....hhhhh..............hhhhhhhhhhhhh......hhhhh...eeee....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...eee......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r8g B   2 PLPDFHVSEPFTLGIELEmQVVNPPGYDLSQDSSmLIDAVKNKITAGEVKH-ITESmLELATDVCRDINQAAGQFSAmQKVVLQAATDHHLEICGGGTHPFQKWQ----------QRTLENFGYLIQQATVFGQHVHVGCASGDDAIYLLHGLSRFVPHFIALSAASPYmQGTDTRFASSRPNIFSAFPDNGPmPWVSNWQQFEALFRCLSYTTmIDSIKDLHWDIRPSPHFGTVEVRVmDTPLTLSHAVNmAGLIQATAHWLLTERPFKHQEKDYLLYKFNRFQACRYGLEGVITDPHTGDRRPLTEDTLRLLEKIAPSAHKIGASSAIEALHRQVVSGLNEAQLmRDFVADGGSLIGLVKKHCEIWA 370
                                    11        21        31    |   41        51| |   | 61        71       |81        91       101    |    -     | 121       131       141       151       161       171       181       191   |   201       211    |  221       231       241       251 |     261       271       281       291       301       311       321       331       341      |351       361         
                                             20-MSE          36-MSE          52 |   |                   79-MSE                    106        117                                                   171-MSE                 195-MSE              216-MSE                  241-MSE     253-MSE                                                                                        348-MSE                  
                                                                               54   |                                                                                                                                                                                                                                                                                                                        
                                                                                   58-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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Glutamine synthetase/guanido kinase (68)

Superfamily: Glutamine synthetase/guanido kinase (68)

Family: Glutamate-cysteine ligase family 2 (GCS2) (2)

Protein domain: Carboxylate-amine ligase YbdK (2)

Escherichia coli [TaxId: 562] (1)

1a	d1r8ga_	A:
1b	d1r8gb_	B:

(no "CATH Domain" information available for 1R8G)

(no "Pfam Domain" information available for 1R8G)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GCS2_ECOLI | P77213)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004357	glutamate-cysteine ligase activity	Catalysis of the reaction: L-cysteine + L-glutamate + ATP = L-gamma-glutamyl-L-cysteine + ADP + 2 H(+) + phosphate.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0016879	ligase activity, forming carbon-nitrogen bonds	Catalysis of the joining of two molecules, or two groups within a single molecule, via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	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:0042398	cellular modified amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of compounds derived from amino acids, organic acids containing one or more amino substituents.

Asymmetric/Biological Unit
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(no "Sites" information available for 1r8g)

	Cis Peptide Bonds
		Pro A:25 - Pro A:26	[ RasMol ]
		Pro B:25 - Pro B:26	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (1, 20)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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Exons (0, 0)

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