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Title :   CRYSTAL STRUCTURE OF PLASMODIUM YOELII ADENOSINE DEAMINASE (PY02076)

Authors :   A. Dong, M. Vedadi, G. Wasney, Y. Zhao, J. Lew, Z. Alam, M. Melone, I. Koeieradzki, A. M. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, A. Bochkarev, R. Hui, M. Amani, Structural Genomics Consortium (Sgc)

Date :   10 Aug 05 (Deposition) - 20 Sep 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.02

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

Keywords :   Plasmodium Yoelii Adenosine Deaminase (Py02076), Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Vedadi, J. Lew, J. Artz, M. Amani, Y. Zhao, A. Dong, G. A. Wasney, M. Gao, T. Hills, S. Brokx, W. Qiu, S. Sharma, A. Diassiti, Z. Alam, M. Melone, A. Mulichak, A. Wernimont, J. Bray, P. Loppnau, O. Plotnikova, K. Newberry, E. Sundararajan, S. Houston, J. Walker, W. Tempel, A. Bochkarev, I. Kozieradzki, A. Edwards, C. Arrowsmith, D. Roos, K. Kain, R. Hui
Genome-Scale Protein Expression And Structural Biology Of Plasmodium Falciparum And Related Apicomplexan Organisms.
Mol. Biochem. Parasitol. V. 151 100 2007
PubMed-ID: 17125854 | Reference-DOI: 10.1016/J.MOLBIOPARA.2006.10.011
(for further references see the PDB file header)

Molecule 1 - ADENOSINE DEAMINASE
	Chains	:	A, B
	EC Number	:	3.5.4.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	P28-LIC-THROMBIN DERIVED FROM PET28
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PLASMODIUM YOELII
	Organism Taxid	:	5861

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 11)

No.	Name	Count	Type	Full Name
1	CO	5	Ligand/Ion	COBALT (II) ION
2	UNX	6	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:55 , HIS A:57 , HIS A:239 , ASP A:323	BINDING SITE FOR RESIDUE CO A 1000
02	AC2	SOFTWARE	HIS A:177 , GLU A:370	BINDING SITE FOR RESIDUE CO A 1002
03	AC3	SOFTWARE	HIS B:55 , HIS B:57 , HIS B:239 , ASP B:323	BINDING SITE FOR RESIDUE CO B 1000
04	AC4	SOFTWARE	HIS B:212 , LEU B:219 , HIS B:222 , HOH B:2177 , HOH B:2205	BINDING SITE FOR RESIDUE CO B 1001
05	AC5	SOFTWARE	ASN B:174 , HIS B:177 , GLU B:370	BINDING SITE FOR RESIDUE CO B 1002
06	AC6	SOFTWARE	HIS A:212 , ILE A:217 , HIS A:222	BINDING SITE FOR RESIDUE UNX A 2000
07	AC7	SOFTWARE	SER A:196 , GLY A:197 , PHE A:210 , VAL A:225 , HOH A:2109	BINDING SITE FOR RESIDUE UNX A 2001
08	AC8	SOFTWARE	ASP A:185 , GLY A:187 , SER A:192	BINDING SITE FOR RESIDUE UNX A 2003
09	AC9	SOFTWARE	HOH A:2047	BINDING SITE FOR RESIDUE UNX A 2004
10	BC1	SOFTWARE	HOH B:2019	BINDING SITE FOR RESIDUE UNX B 2005

(no "SS Bond" information available for 2AMX)

(no "Cis Peptide Bond" information available for 2AMX)

(no "SAP(SNP)/Variant" information available for 2AMX)

(no "PROSITE Motif" information available for 2AMX)

(no "Exon" information available for 2AMX)

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:364
 aligned with Q7RMV2_PLAYO | Q7RMV2 from UniProtKB/TrEMBL  Length:364

    Alignment length:364
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360    
         Q7RMV2_PLAYO     1 MMEIPTEEIKFLKKEDVQNIDLNGMSKKERYEIWRRIPKVELHCHLDLTFSAEFFLKWARKYNLQPNMSDDEILDHYLFTKEGKSLAEFIRKAISVSDLYRDYDFIEDLAKWAVIEKYKEGVVLMEFRYSPTFVSSSYGLDVELIHKAFIKGIKNATELLNNKIHVALICISDTGHAAASIKHSGDFAIKHKHDFVGFDHGGREIDLKDHKDVYHSVRDHGLHLTVHAGEDATLPNLNTLYTAINILNVERIGHGIRVSESDELIELVKKKDILLEVCPISNLLLNNVKSMDTHPIRKLYDAGVKVSVNSDDPGMFLSNINDNYEKLYIHLNFTLEEFMIMNNWAFEKSFVSDDVKSELKALYF 364
               SCOP domains -------d2amxa1 A:20-376 Adenosine deaminase (ADA)                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh............hhhhhhhhhhhhhhhhh.eee...hhhhh.hhhhhhhhhhhh......hhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.eeeeeeeehhhhhhhh...hhhhhhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhh.hhhhhhh...eeeee.......hhhhhhhhhhhhhh..eeeeee........hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhh.eeeehhhhhhhh.........hhhhhhhh..eeee...hhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2amx A  13 GLVPRGSEIKFLKKEDVQNIDLNGMSKKERYEIWRRIPKVELHCHLDLTFSAEFFLKWARKYNLQPNMSDDEILDHYLFTKEGKSLAEFIRKAISVSDLYRDYDFIEDLAKWAVIEKYKEGVVLMEFRYSPTFVSSSYGLDVELIHKAFIKGIKNATELLNNKIHVALICISDTGHAAASIKHSGDFAIKHKHDFVGFDHGGREIDLKDHKDVYHSVRDHGLHLTVHAGEDATLPNLNTLYTAINILNVERIGHGIRVSESDELIELVKKKDILLEVCPISNLLLNNVKSMDTHPIRKLYDAGVKVSVNSDDPGMFLSNINDNYEKLYIHLNFTLEEFMIMNNWAFEKSFVSDDVKSELKALYF 376
                                    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

Chain B from PDB  Type:PROTEIN  Length:356
 aligned with Q7RMV2_PLAYO | Q7RMV2 from UniProtKB/TrEMBL  Length:364

    Alignment length:364
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360    
         Q7RMV2_PLAYO     1 MMEIPTEEIKFLKKEDVQNIDLNGMSKKERYEIWRRIPKVELHCHLDLTFSAEFFLKWARKYNLQPNMSDDEILDHYLFTKEGKSLAEFIRKAISVSDLYRDYDFIEDLAKWAVIEKYKEGVVLMEFRYSPTFVSSSYGLDVELIHKAFIKGIKNATELLNNKIHVALICISDTGHAAASIKHSGDFAIKHKHDFVGFDHGGREIDLKDHKDVYHSVRDHGLHLTVHAGEDATLPNLNTLYTAINILNVERIGHGIRVSESDELIELVKKKDILLEVCPISNLLLNNVKSMDTHPIRKLYDAGVKVSVNSDDPGMFLSNINDNYEKLYIHLNFTLEEFMIMNNWAFEKSFVSDDVKSELKALYF 364
               SCOP domains d2amxb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh............hhhhhhhhhhhhhhhhh.eeeeeee.hhh.hhhhhhhhhhhh......hhhhhhhhhh......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.eeeeeeeehhhhhhhh...hhhhhhhhhhhhhhhhhh......eeeeeee..--------hhhhhhhhhh...eeeee.......hhhhhhhhhhhhhh..eeeeee........hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhh.eeeehhhhhhhh.........hhhhhhhh..eeee...hhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2amx B  13 GLVPRGSEIKFLKKEDVQNIDLNGMSKKERYEIWRRIPKVELHCHLDLTFSAEFFLKWARKYNLQPNMSDDEILDHYLFTKEGKSLAEFIRKAISVSDLYRDYDFIEDLAKWAVIEKYKEGVVLMEFRYSPTFVSSSYGLDVELIHKAFIKGIKNATELLNNKIHVALICISD--------KHSGDFAIKHKHDFVGFDHGGREIDLKDHKDVYHSVRDHGLHLTVHAGEDATLPNLNTLYTAINILNVERIGHGIRVSESDELIELVKKKDILLEVCPISNLLLNNVKSMDTHPIRKLYDAGVKVSVNSDDPGMFLSNINDNYEKLYIHLNFTLEEFMIMNNWAFEKSFVSDDVKSELKALYF 376
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182  |      - |     202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372    
                                                                                                                                                                                                      185      194

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Metallo-dependent hydrolases (273)

Family: Adenosine/AMP deaminase (36)

Protein domain: Adenosine deaminase (ADA) (24)

Plasmodium yoelii [TaxId: 5861] (1)

d2amxa1

A:20-376

Protein domain: automated matches (11)

Plasmodium yoelii [TaxId: 5861] (1)

d2amxb_

(no "CATH Domain" information available for 2AMX)

(no "Pfam Domain" information available for 2AMX)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q7RMV2_PLAYO | Q7RMV2)

molecular function
	GO:0019239	deaminase activity	Catalysis of the removal of an amino group from a substrate, producing ammonia (NH3).
biological process
	GO:0009168	purine ribonucleoside monophosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of purine ribonucleoside monophosphate, a compound consisting of a purine base linked to a ribose sugar esterified with phosphate on the sugar.

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (2, 11)

Sites (10, 10)

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