1MJH - JenaLib

Title :   STRUCTURE-BASED ASSIGNMENT OF THE BIOCHEMICAL FUNCTION OF HYPOTHETICAL PROTEIN MJ0577: A TEST CASE OF STRUCTURAL GENOMICS

Authors :   T. I. Zarembinski, L. -W. Hung, H. J. Mueller-Dieckmann, K. -K. Kim, H. Yokota, R. Kim, S. -H. Kim, Berkeley Structural Genomics Center (Bsgc)

Date :   04 Nov 98 (Deposition) - 23 Dec 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Hypothetical Protein, Structural Genomics, Functional Assignment, Atp Binding Protein, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. I. Zarembinski, L. -W. Hung, H. J. Mueller-Dieckmann, K. -K. Kim, H. Yokota, R. Kim, S. -H. Kim
Structure-Based Assignment Of The Biochemical Function Of A Hypothetical Protein: A Test Case Of Structural Genomics.
Proc. Natl. Acad. Sci. Usa V. 95 15189 1998
PubMed-ID: 9860944 | Reference-DOI: 10.1073/PNAS.95.26.15189
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ATP A:2001 , HOH A:4009 , HOH A:4010 , HOH A:4019	BINDING SITE FOR RESIDUE MN A 4001
2	AC2	SOFTWARE	HOH B:8 , HOH B:15 , HOH B:28 , ATP B:3001	BINDING SITE FOR RESIDUE MN B 4002
3	AC3	SOFTWARE	PRO A:11 , THR A:12 , ASP A:13 , LEU A:39 , VAL A:41 , PRO A:108 , MET A:126 , GLY A:127 , HIS A:129 , GLY A:130 , LYS A:131 , THR A:132 , ASN A:133 , GLY A:140 , SER A:141 , VAL A:142 , THR A:143 , MN A:4001 , HOH A:4004 , HOH A:4012 , HOH A:4017 , HOH A:4025 , HOH A:4083	BINDING SITE FOR RESIDUE ATP A 2001
4	AC4	SOFTWARE	HOH B:6 , HOH B:11 , HOH B:15 , HOH B:24 , HOH B:62 , HOH B:115 , HOH B:133 , PRO B:1011 , THR B:1012 , ASP B:1013 , ALA B:1018 , VAL B:1041 , PRO B:1108 , MET B:1126 , GLY B:1127 , HIS B:1129 , GLY B:1130 , LYS B:1131 , THR B:1132 , ASN B:1133 , GLY B:1140 , SER B:1141 , VAL B:1142 , THR B:1143 , MN B:4002	BINDING SITE FOR RESIDUE ATP B 3001

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:143
 aligned with Y577_METJA | Q57997 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:160
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162
          Y577_METJA      3 VMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRKNS  162
               SCOP domains d1mjha_ A: Hypothetical protein MJ0577                                                                                                                           SCOP domains
               CATH domains 1mjhA00 A:3-162 Tyrosyl-Transfer RNA Synthetas                 e , subunit E, domain 1                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhh......eeeeeeeeehhh..-----------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee.hhhhhhhhhhh.....eeee.............hhhhhhhhh....eeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1mjh A    3 VMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIK-----------------VEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRKNS  162
                                    12        22        32        42     |   -         -   |    72        82        92       102       112       122       132       142       152       162
                                                                        48                66

Chain B from PDB  Type:PROTEIN  Length:144
 aligned with Y577_METJA | Q57997 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:160
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162
          Y577_METJA      3 VMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRKNS  162
               SCOP domains d1mjhb_ B: Hypothetical protein MJ0577                                                                                                                           SCOP domains
               CATH domains 1mjhB00 B:1003-1162 Tyrosyl-Transfer RNA Synth                etase , subunit E, domain 1                                                                        CATH domains
           Pfam domains (1) -Usp-1mjhB01 B:1004-1158                                                                                                                                    ---- Pfam domains (1)
           Pfam domains (2) -Usp-1mjhB02 B:1004-1158                                                                                                                                    ---- Pfam domains (2)
         Sec.struct. author ....eeeee....hhhhhhhhhhhhh......eeeeeeeeehhhh.----------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee.hhhhhhhhhhh.....eeee.............hhhhhhhhh....eeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1mjh B 1003 VMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIK----------------SVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRKNS 1162
                                  1012      1022      1032      1042     |   -         -  |   1072      1082      1092      1102      1112      1122      1132      1142      1152      1162
                                                                      1048             1065

Legend:		→ Mismatch	(orange background)
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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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Y577_METJA | Q57997)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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:0006950	response to stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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