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Title :   CRYSTAL STRUCTURE OF ADENINE PHOSPHORIBOSYLTRANSFERASE FROM RHODOTHERMUS MARINUS DSM 4252, NYSGRC TARGET 029775.

Authors :   V. N. Malashkevich, R. Bhosle, R. Toro, B. Hillerich, A. Gizzi, S. Garfo A. Kar, M. K. Chan, J. Lafluer, H. Patel, B. Matikainen, S. Chamala, S. L A. Celikgil, G. Villegas, B. Evans, J. Love, A. Fiser, K. Khafizov, R. S J. B. Bonanno, S. C. Almo, New York Structural Genomics Research Consortium (Nysgrc)

Date :   01 Aug 13 (Deposition) - 14 Aug 13 (Release) - 14 Aug 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Structural Genomics, Protein Structure Initiative, Nysgrc, Adenine Phosphoribosyltransferase, Psi-Biology, New York Structural Genomics Research Consortium, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. N. Malashkevich, R. Bhosle, R. Toro, B. Hillerich, A. Gizzi, S. Garforth, A. Kar, M. K. Chan, J. Lafluer, H. Patel, B. Matikainen, S. Chamala, S. Lim, A. Celikgil, G. Villegas, B. Evans, J. Love, A. Fiser, K. Khafizov, R. Seidel, J. B. Bonanno, S. C. Almo
Crystal Structure Of Adenine Phosphoribosyltransferase From Rhodothermus Marinus Dsm 4252, Nysgrc Target 029775.
To Be Published
PubMed: search

Molecule 1 - ADENINE PHOSPHORIBOSYLTRANSFERASE
	Chains	:	A, B, C, D
	EC Number	:	2.4.2.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BC-PSGX3(BC)
	Expression System Strain	:	BL21(DE3)CODON+RIL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	268316379, APT, RMAR_0813
	Organism Scientific	:	RHODOTHERMUS MARINUS
	Organism Taxid	:	518766
	Strain	:	DSM 4252
	Synonym	:	APRT

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 16)

No.	Name	Count	Type	Full Name
1	AMP	4	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	CA	4	Ligand/Ion	CALCIUM ION
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:25 , PHE A:26 , LYS A:27 , GLU A:62 , ASP A:124 , ASP A:125 , VAL A:126 , ALA A:128 , THR A:129 , GLY A:130 , GLY A:131 , THR A:132 , LEU A:156 , HOH A:415 , HOH A:421 , HOH A:426 , HOH A:427 , HOH A:444 , HOH A:490 , HOH A:555	BINDING SITE FOR RESIDUE AMP A 300
2	AC2	SOFTWARE	ASP A:77 , HOH A:472 , HOH A:474 , HOH A:521 , HOH A:522	BINDING SITE FOR RESIDUE CA A 301
3	AC3	SOFTWARE	GLN B:25 , PHE B:26 , LYS B:27 , ASP B:124 , ASP B:125 , VAL B:126 , ALA B:128 , THR B:129 , GLY B:130 , GLY B:131 , THR B:132 , LEU B:156 , HOH B:402 , HOH B:407 , HOH B:416 , HOH B:417 , HOH B:451 , HOH B:480 , HOH B:488 , HOH B:490	BINDING SITE FOR RESIDUE AMP B 300
4	AC4	SOFTWARE	HOH B:456 , HOH B:466 , HOH B:478 , HOH B:495 , HOH B:544 , HOH B:548	BINDING SITE FOR RESIDUE CA B 301
5	AC5	SOFTWARE	GLN C:25 , PHE C:26 , LYS C:27 , ASP C:124 , ASP C:125 , VAL C:126 , ALA C:128 , THR C:129 , GLY C:130 , GLY C:131 , THR C:132 , LEU C:156 , HOH C:303 , HOH C:311 , HOH C:315 , HOH C:316 , HOH C:391 , HOH C:398 , HOH C:404 , HOH C:469	BINDING SITE FOR RESIDUE AMP C 201
6	AC6	SOFTWARE	GLN B:11 , HOH B:409 , HOH B:437 , GLU C:134 , HOH C:331 , HOH C:368	BINDING SITE FOR RESIDUE CA C 202
7	AC7	SOFTWARE	GLN D:25 , PHE D:26 , LYS D:27 , ASP D:124 , ASP D:125 , VAL D:126 , ALA D:128 , THR D:129 , GLY D:130 , GLY D:131 , THR D:132 , LEU D:156 , HOH D:412 , HOH D:419 , HOH D:440 , HOH D:475 , HOH D:482 , HOH D:489 , HOH D:503 , HOH D:529	BINDING SITE FOR RESIDUE AMP D 300
8	AC8	SOFTWARE	GLU A:134 , GLN D:11 , HOH D:427 , HOH D:464 , HOH D:496 , HOH D:498	BINDING SITE FOR RESIDUE CA D 301

(no "SS Bond" information available for 4M0K)

Asymmetric Unit

No.	Residues
1	Phe A:19	-	Pro A:20
2	Phe B:19	-	Pro B:20
3	Phe C:19	-	Pro C:20
4	Phe D:19	-	Pro D:20

(no "SAP(SNP)/Variant" information available for 4M0K)

(no "PROSITE Motif" information available for 4M0K)

(no "Exon" information available for 4M0K)

Asymmetric 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)
	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:173
                                                                                                                                                                                                             
               SCOP domains d4m0ka_ A: automated matches                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhheeee.......eeeehhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhh..eeeeeee.......eeeeeee....eeeeeee........eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeeee.hhhhhhhh.....eeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m0k A   5 ALETLKQAIRTVPDFPEPGIQFKDITPVLGHPELLRLAIEALLEPFQEQEITKVVGIESRGFILGGmLAHHLDAGFVPVRKKGKLPYQTLAESYQLEYGTDTIEmHIDAIEPGDRVLIHDDVIATGGTAEATIRLVERAGGEVVGCAFLIELTGLQGRKRLPAHVPVHTVLQL 177
                                    14        24        34        44        54        64      | 74        84        94       104    |  114       124       134       144       154       164       174   
                                                                                             71-MSE                               109-MSE

Chain B from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains d4m0kb_ B: automated matches                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhheeee.......eeeehhhhhhhhhhhhhhhhhhhh........eeeeehhhhhhhhhhhhhhh..eeeeeee.......eeeeeee....eeeeeee........eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeeee...hhhhhh.....eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4m0k B   4 TALETLKQAIRTVPDFPEPGIQFKDITPVLGHPELLRLAIEALLEPFQEQEITKVVGIESRGFILGGmLAHHLDAGFVPVRKKGKLPYQTLAESYQLEYGTDTIEmHIDAIEPGDRVLIHDDVIATGGTAEATIRLVERAGGEVVGCAFLIELTGLQGRKRLPAHVPVHTVLQL 177
                                    13        23        33        43        53        63       |73        83        93       103     | 113       123       133       143       153       163       173    
                                                                                              71-MSE                               109-MSE

Chain C from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               SCOP domains d4m0kc_ C: automated matches                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhheeee.......eeeehhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhh..eeeeeee.......eeeeeee....eeeeeee........eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeeee.hhhhhhhh.....eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m0k C   2 NATALETLKQAIRTVPDFPEPGIQFKDITPVLGHPELLRLAIEALLEPFQEQEITKVVGIESRGFILGGmLAHHLDAGFVPVRKKGKLPYQTLAESYQLEYGTDTIEmHIDAIEPGDRVLIHDDVIATGGTAEATIRLVERAGGEVVGCAFLIELTGLQGRKRLPAHVPVHTVLQL 177
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171      
                                                                                                71-MSE                               109-MSE

Chain D from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               SCOP domains d4m0kd_ D: automated matches                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhheee.........eeehhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhh.eeeeeee.......eeee..ee..ee..eeee........eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeeee...hhhhhh.....eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m0k D   2 NATALETLKQAIRTVPDFPEPGIQFKDITPVLGHPELLRLAIEALLEPFQEQEITKVVGIESRGFILGGmLAHHLDAGFVPVRKKGKLPYQTLAESYQLEYGTDTIEmHIDAIEPGDRVLIHDDVIATGGTAEATIRLVERAGGEVVGCAFLIELTGLQGRKRLPAHVPVHTVLQL 177
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171      
                                                                                                71-MSE                               109-MSE

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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

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Class: Alpha and beta proteins (a/b) (23833)

Fold: PRTase-like (145)

Superfamily: PRTase-like (145)

Family: automated matches (39)

Protein domain: automated matches (39)

Rhodothermus marinus [TaxId: 518766] (1)

1a	d4m0ka_	A:
1b	d4m0kb_	B:
1c	d4m0kc_	C:
1d	d4m0kd_	D:

(no "CATH Domain" information available for 4M0K)

(no "Pfam Domain" information available for 4M0K)

Asymmetric Unit(hide GO term definitions)

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		Phe C:19 - Pro C:20	[ RasMol ]
		Phe D:19 - Pro D:20	[ RasMol ]

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Ligands, Modified Residues, Ions (3, 16)

Sites (8, 8)

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Cis Peptide Bonds (4, 4)

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