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Title :   CRYSTAL STRUCTURE OF APC1665, YUAD PROTEIN FROM BACILLUS SUBTILIS

Authors :   Y. Kim, A. Joachimiak, A. Edwards, T. Skarina, A. Savchenko, Midwest Center For Structural Genomics (Mcsg)

Date :   15 Mar 03 (Deposition) - 23 Sep 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Structural Genomics, Yuad Protein, Cytosolic Hypothetical Protein, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kim, A. Joachimiak, A. Edwards, T. Skarina, A. Savchenko
Crystal Structure Of Apc1665, Yuad Protein From Bacillus Subtilis
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - YUAD PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Taxid	:	562
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 18)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:40 , LYS A:45 , ARG A:50 , HOH A:623	BINDING SITE FOR RESIDUE SO4 A 501
2	AC2	SOFTWARE	ARG A:166 , LYS B:8 , THR B:58 , GLU B:59 , GLY B:173	BINDING SITE FOR RESIDUE SO4 B 502
3	AC3	SOFTWARE	LYS B:45 , ARG B:50 , ARG B:64 , HOH B:565 , HOH B:593 , HOH B:674	BINDING SITE FOR RESIDUE SO4 B 503
4	AC4	SOFTWARE	ARG B:50 , ASP B:127 , CYS B:129 , PRO B:132 , ARG B:158	BINDING SITE FOR RESIDUE CL B 505
5	AC5	SOFTWARE	ARG A:50 , CYS A:129 , PRO A:132 , ARG A:158	BINDING SITE FOR RESIDUE CL A 506

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

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

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MOSC	PS51340	MOSC domain profile.	YUAD_BACSU	15-179	2	A:15-179 B:15-179

(no "Exon" information available for 1ORU)

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:182
 aligned with YUAD_BACSU | O32079 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  
           YUAD_BACSU     1 MWKRMTAKAEGLYIADTKSFVTKQMDKLDFDYGGIPGDLHFGLTKKAGAREPMFSRGTEIFNRRQISIVSIEECNEIALKMGVPRILPEWLGANVAVSGMPDLTSLKEGSRIIFPSGAALLCEGENDPCIQPGEVIQSYYPDQPKLASAFVRHALGIRGIVCIVERPGAVYTGDEIEVHSYQ 182
               SCOP domains d1orua_ A: Hypothetical protein YuaD                                                                                                                                                   SCOP domains
               CATH domains -1oruA00 A:2-182 PK beta-barrel domain-like                                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........eee.eeee.............eee............eee....eeeeehhhhhhhhhhhh....hhhhhh..eeee...hhhhh....eee.....eeeeeee...hhhhhhhhhhhh....hhhhhhhhhh.....eeeeeee.eeee...eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------MOSC  PDB: A:15-179 UniProt: 15-179                                                                                                                                  --- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oru A   1 mWKRmTAKAEGLYIADTKSFVTKQmDKLDFDYGGIPGDLHFGLTKKAGAREPmFSRGTEIFNRRQISIVSIEECNEIALKmGVPRILPEWLGANVAVSGmPDLTSLKEGSRIIFPSGAALLCEGENDPCIQPGEVIQSYYPDQPKLASAFVRHALGIRGIVCIVERPGAVYTGDEIEVHSYQ 182
                            |   |   10        20    |   30        40        50  |     60        70        80|       90       100       110       120       130       140       150       160       170       180  
                            |   |                  25-MSE                      53-MSE                      81-MSE            100-MSE                                                                              
                            1-MSE                                                                                                                                                                                 
                                5-MSE

Chain B from PDB  Type:PROTEIN  Length:182
 aligned with YUAD_BACSU | O32079 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  
           YUAD_BACSU     1 MWKRMTAKAEGLYIADTKSFVTKQMDKLDFDYGGIPGDLHFGLTKKAGAREPMFSRGTEIFNRRQISIVSIEECNEIALKMGVPRILPEWLGANVAVSGMPDLTSLKEGSRIIFPSGAALLCEGENDPCIQPGEVIQSYYPDQPKLASAFVRHALGIRGIVCIVERPGAVYTGDEIEVHSYQ 182
               SCOP domains d1orub_ B: Hypothetical protein YuaD                                                                                                                                                   SCOP domains
               CATH domains -1oruB00 B:2-182 PK beta-barrel domain-like                                                                                                                                            CATH domains
           Pfam domains (1) ---------------------------------MOSC-1oruB01 B:34-178                                                                                                                            ---- Pfam domains (1)
           Pfam domains (2) ---------------------------------MOSC-1oruB02 B:34-178                                                                                                                            ---- Pfam domains (2)
         Sec.struct. author .eeeeeeeeeeeee........ee..eeee.............eee............eee....eeeeehhhhhhhhhhhh....hhhhhh..eeee...hhhhh....eee.....eeeeeee...hhhhhhhhhhhh....hhhhhhhhhhh....eeeeeee.eeee...eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------MOSC  PDB: B:15-179 UniProt: 15-179                                                                                                                                  --- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oru B   1 mWKRmTAKAEGLYIADTKSFVTKQmDKLDFDYGGIPGDLHFGLTKKAGAREPmFSRGTEIFNRRQISIVSIEECNEIALKmGVPRILPEWLGANVAVSGmPDLTSLKEGSRIIFPSGAALLCEGENDPCIQPGEVIQSYYPDQPKLASAFVRHALGIRGIVCIVERPGAVYTGDEIEVHSYQ 182
                            |   |   10        20    |   30        40        50  |     60        70        80|       90       100       110       120       130       140       150       160       170       180  
                            1-MSE                  25-MSE                      53-MSE                      81-MSE            100-MSE                                                                              
                                5-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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PK beta-barrel domain-like (31)

Superfamily: PK beta-barrel domain-like (31)

Family: MOSC (MOCO sulphurase C-terminal) domain (3)

Protein domain: Hypothetical protein YuaD (1)

Bacillus subtilis [TaxId: 1423] (1)

1a	d1orua_	A:
1b	d1orub_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: M1 Pyruvate Kinase; Domain 3 (24)

Homologous Superfamily: PK beta-barrel domain-like (3)

Bacillus subtilis. Organism_taxid: 1423. (1)

1a	1oruA00	A:2-182
1b	1oruB00	B:2-182

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: MOSC] (3)

Family: MOSC (3)

Bacillus subtilis (1)

1a	MOSC-1oruB01	B:34-178
1b	MOSC-1oruB02	B:34-178

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (YUAD_BACSU | O32079)


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:0030151	molybdenum ion binding	Interacting selectively and non-covalently with molybdenum (Mo) ions.
GO:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (3, 18)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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