3USB - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS INOSINE MONOPHOSPHATE DEHYDROGENASE IN THE COMPLEX WITH IMP

Authors :   Y. Kim, R. Zhang, R. Wu, M. Gu, W. F. Anderson, A. Joachimiak, Csgid, Cent Structural Genomics Of Infectious Diseases (Csgid)

Date :   23 Nov 11 (Deposition) - 07 Dec 11 (Release) - 24 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.38

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (4x)
Biol. Unit 2: B  (4x)
Biol. Unit 3: A (4x),B (4x)

Keywords :   Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Tim Barrel, Cbs-Domain, Cytosol, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Makowska-Grzyska, Y. Kim, R. Wu, R. Wilton, D. R. Gollapalli, X. K. Wang, R. Zhang, R. Jedrzejczak, J. C. Mack, N. Maltseva, R. Mulligan, T. A. Binkowski, P. Gornicki, M. L. Kuhn, W. F. Anderson, L. Hedstrom, A. Joachimiak
Bacillus Anthracis Inosine 5'-Monophosphate Dehydrogenase I Action: The First Bacterial Series Of Structures Of Phosphate Ion-, Substrate-, And Product-Bound Complexes.
Biochemistry V. 51 6148 2012
PubMed-ID: 22788966 | Reference-DOI: 10.1021/BI300511W

Molecule 1 - INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.205
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21 MAGIC
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	GUAB, BA_0008, BAS0011, GBAA_0008
	Organism Common	:	ANTHRAX,ANTHRAX BACTERIUM
	Organism Scientific	:	BACILLUS ANTHRACIS
	Organism Taxid	:	198094
	Strain	:	AMES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 36)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	GOL	4	Ligand/Ion	GLYCEROL
3	IMP	2	Ligand/Ion	INOSINIC ACID
4	MSE	27	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 72)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	8	Ligand/Ion	GLYCEROL
3	IMP	4	Ligand/Ion	INOSINIC ACID
4	MSE	56	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 68)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	8	Ligand/Ion	GLYCEROL
3	IMP	4	Ligand/Ion	INOSINIC ACID
4	MSE	52	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 3 (4, 68)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	8	Ligand/Ion	GLYCEROL
3	IMP	4	Ligand/Ion	INOSINIC ACID
4	MSE	52	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:49 , MSE A:51 , GLY A:305 , SER A:306 , ILE A:307 , CYS A:308 , ASP A:341 , GLY A:342 , GLY A:343 , MSE A:362 , GLY A:364 , SER A:365 , HOH A:559 , HOH A:561 , HOH A:617 , HOH A:640 , HOH A:728	BINDING SITE FOR RESIDUE IMP A 500
2	AC2	SOFTWARE	ARG A:65 , ARG A:119 , LYS A:202 , LYS A:206	BINDING SITE FOR RESIDUE SO4 A 501
3	AC3	SOFTWARE	PRO A:27 , HIS A:254 , ALA A:441 , TYR A:445 , HOH A:692	BINDING SITE FOR RESIDUE GOL A 502
4	AC4	SOFTWARE	GLU A:9 , THR A:322 , HOH A:601 , HOH A:744	BINDING SITE FOR RESIDUE GOL A 503
5	AC5	SOFTWARE	ALA B:49 , SER B:306 , ILE B:307 , CYS B:308 , ASP B:341 , GLY B:342 , GLY B:343 , MSE B:362 , GLY B:364 , SER B:365 , HOH B:544 , HOH B:574 , HOH B:631 , HOH B:632 , HOH B:635	BINDING SITE FOR RESIDUE IMP B 500
6	AC6	SOFTWARE	SER B:23 , PRO B:27 , HIS B:254 , ALA B:441 , GLY B:444 , TYR B:445	BINDING SITE FOR RESIDUE GOL B 501
7	AC7	SOFTWARE	LYS B:8 , GLU B:9 , ASP B:326 , HOH B:522 , HOH B:604 , HOH B:643	BINDING SITE FOR RESIDUE GOL B 502
8	AC8	SOFTWARE	PHE B:6 , LEU B:11 , THR B:322 , HOH B:522	BINDING SITE FOR RESIDUE SO4 B 503
9	AC9	SOFTWARE	THR B:12 , PRO B:304 , GLN B:320	BINDING SITE FOR RESIDUE CL B 504

(no "SS Bond" information available for 3USB)

Asymmetric Unit

No.	Residues
1	Gly A:279	-	Asn A:280
2	Gly B:279	-	Asn B:280

(no "SAP(SNP)/Variant" information available for 3USB)

(no "PROSITE Motif" information available for 3USB)

(no "Exon" information available for 3USB)

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:442
 aligned with Q81W29_BACAN | Q81W29 from UniProtKB/TrEMBL  Length:487

    Alignment length:476
                                   1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463      
         Q81W29_BACAN     - -------MWESKFVKEGLTFDDVLLVPAKSDVLPREVSVKTVLSESLQLNIPLISAGMDTVTEADMAIAMARQGGLGIIHKNMSIEQQAEQVDKVKRSESGVISDPFFLTPEHQVYDAEHLMGKYRISGVPVVNNLDERKLVGIITNRDMRFIQDYSIKISDVMTKEQLITAPVGTTLSEAEKILQKYKIEKLPLVDNNGVLQGLITIKDIEKVIEFPNSAKDKQGRLLVGAAVGVTADAMTRIDALVKASVDAIVLDTAHGHSQGVIDKVKEVRAKYPSLNIIAGNVATAEATKALIEAGANVVKVGIGPGSICTTRVVAGVGVPQLTAVYDCATEARKHGIPVIADGGIKYSGDMVKALAAGAHVVMLGSMFAGVAESPGETEIYQGRQFKVYRGMGSVGAMEKGSKDRYFQEGNKKLVPEGIEGRVPYKGPLADTVHQLVGGLRAGMGYCGAQDLEFLRENAQFIRMSGAGLL 469
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh.......hhh.eee...............eeee..eee...eee.......hhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh................hhhhhhhhhhhhh..eeeee.......eeeeeehhhhh.......hhhhhh.......ee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhh.............eeee....hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh..eeee........hhhhhhh...hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhh...eeee............eeee....eeee----------------------------------.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.eee.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3usb A  -6 LYFQSNAmWESKFVKEGLTFDDVLLVPAKSDVLPREVSVKTVLSESLQLNIPLISAGmDTVTEADmAIAmARQGGLGIIHKNmSIEQQAEQVDKVKRSESGVISDPFFLTPEHQVYDAEHLmGKYRISGVPVVNNLDERKLVGIITNRDmRFIQDYSIKISDVmTKEQLITAPVGTTLSEAEKILQKYKIEKLPLVDNNGVLQGLITIKDIEKVIEFPNSAKDKQGRLLVGAAVGVTADAmTRIDALVKASVDAIVLDTAHGHSQGVIDKVKEVRAKYPSLNIIAGNVATAEATKALIEAGANVVKVGIGPGSICTTRVVAGVGVPQLTAVYDCATEARKHGIPVIADGGIKYSGDmVKALAAGAHVVmLGSmFAGVAESPGETEIYQGRQFKV----------------------------------VPYKGPLADTVHQLVGGLRAGmGYCGAQDLEFLRENAQFIRmSGAGLL 469
                                   | 3        13        23        33        43       |53     |  63        73  |     83        93       103       113 |     123       133       143       153   |   163       173       183       193       203       213       223       233|      243       253       263       273       283       293       303       313       323       333       343      |353       363  |    373       383   |     -         -         -       423       433       443       453       463      
                                   1-MSE                                            51-MSE  59-MSE           76-MSE                                115-MSE                     143-MSE       157-MSE                                                                      234-MSE                                                                                                             350-MSE     362-MSE                  387                                422                  443-MSE             463-MSE  
                                                                                                63-MSE                                                                                                                                                                                                                                                                                                        366-MSE

Chain B from PDB  Type:PROTEIN  Length:401
 aligned with Q81W29_BACAN | Q81W29 from UniProtKB/TrEMBL  Length:487

    Alignment length:477
                                    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       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       
         Q81W29_BACAN     - --------MWESKFVKEGLTFDDVLLVPAKSDVLPREVSVKTVLSESLQLNIPLISAGMDTVTEADMAIAMARQGGLGIIHKNMSIEQQAEQVDKVKRSESGVISDPFFLTPEHQVYDAEHLMGKYRISGVPVVNNLDERKLVGIITNRDMRFIQDYSIKISDVMTKEQLITAPVGTTLSEAEKILQKYKIEKLPLVDNNGVLQGLITIKDIEKVIEFPNSAKDKQGRLLVGAAVGVTADAMTRIDALVKASVDAIVLDTAHGHSQGVIDKVKEVRAKYPSLNIIAGNVATAEATKALIEAGANVVKVGIGPGSICTTRVVAGVGVPQLTAVYDCATEARKHGIPVIADGGIKYSGDMVKALAAGAHVVMLGSMFAGVAESPGETEIYQGRQFKVYRGMGSVGAMEKGSKDRYFQEGNKKLVPEGIEGRVPYKGPLADTVHQLVGGLRAGMGYCGAQDLEFLRENAQFIRMSGAGLL 469
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh.......hhh.eee.......hhhhh...eeee..eee...eee.......hhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhh.............----------------....-----------..hhhhhh..------.................hhhhhhhhhhhhh..ee..---------.eehhhhhhhhhh.............eeeee...hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhh...eeee........hhhhhhh...hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeee............eeee....eeee----------------------------------.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.eee.hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3usb B  -7 NLYFQSNAmWESKFVKEGLTFDDVLLVPAKSDVLPREVSVKTVLSESLQLNIPLISAGmDTVTEADmAIAmARQGGLGIIHKNmSIEQQAEQVDKVKRSESGVISDPFFLTPE----------------GVPV-----------IITNRDmRFI------ISDVmTKEQLITAPVGTTLSEAEKILQKYKIEKLPL---------LITIKDIEKVIEFPNSAKDKQGRLLVGAAVGVTADAmTRIDALVKASVDAIVLDTAHGHSQGVIDKVKEVRAKYPSLNIIAGNVATAEATKALIEAGANVVKVGIGPGSICTTRVVAGVGVPQLTAVYDCATEARKHGIPVIADGGIKYSGDmVKALAAGAHVVmLGSmFAGVAESPGETEIYQGRQFKV----------------------------------VPYKGPLADTVHQLVGGLRAGmGYCGAQDLEFLRENAQFIRmSGAGLL 469
                                    |2        12        22        32        42        52      | 62|       72   |    82        92       102  |      -       122  |      -    |  142|  |     -|   |  162       172       182     |   -     | 202       212       222       232 |     242       252       262       272       282       292       302       312       322       332       342       352       362   |   372       382    |    -         -         -       422       432       442|      452       462|      
                                    1-MSE                                            51-MSE  59-MSE           76-MSE                      105              122  |         137     |  |    153   |                            188       198                                 234-MSE                                                                                                             350-MSE     362-MSE                  387                                422                  443-MSE             463-MSE  
                                                                                                 63-MSE                                                       125               143-MSE       157-MSE                                                                                                                                                                                                          366-MSE                                                                                                   
                                                                                                                                                                                   146

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 '\|'

(no "SCOP Domain" information available for 3USB)

(no "CATH Domain" information available for 3USB)

(no "Pfam Domain" information available for 3USB)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q81W29_BACAN | Q81W29)

molecular function
	GO:0003938	IMP dehydrogenase activity	Catalysis of the reaction: inosine 5'-phosphate + NAD+ + H2O = xanthosine 5'-phosphate + NADH + H+.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0006177	GMP biosynthetic process	The chemical reactions and pathways resulting in the formation of GMP, guanosine monophosphate.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006164	purine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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	Cis Peptide Bonds
		Gly A:279 - Asn A:280	[ RasMol ]
		Gly B:279 - Asn B:280	[ RasMol ]

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	3usb
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3stb	THE SAME PROTEIN, APO-FORM
3std	THE SAME PROTEIN, COMPLEXED WITH XMP RELATED ID: IDP01178 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 36)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (8, 8)

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